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NAR Web Server Summaries - Alphabetical List

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2can Bioinformatics Educational Resource
The site contains tutorials, a glossary, and introductory articles on various topics related to bioinformatics and molecular and cell biology. The emphasis is on an increased understanding of the databases and tools available...
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3D-DART
The 3D-DART web server interfaces to a collection of tools for the generation of DNA structural models in custom conformations.
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3D-Footprint
3D-footprint provides estimates of binding specificity for all protein-DNA complexes available at the Protein Data Bank. The web interface allows the user to: (i) browse DNA-binding proteins by keyword; (ii) find proteins tha...
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3D-Fun
3D-Fun is software for predicting enzyme function from structure rather than sequence. Users input protein coordinates in PDB format to which all known protein structures are compared by 3D structural superposition. Superposi...
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3did
The database of three-dimensional interacting domains (3did) is a collection of protein interactions for which high-resolution three-dimensional structures are known. The interface residues are presented for each interaction ...
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3DLigandSite
3DLigandSite is a web server for the prediction of ligand binding sites. Ligands bound to similar protein structures as the query structure are used to predict the binding site.
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3dLOGO
3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.
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3DNALandscapes
3DNALandscapes is a database for exploring the conformational features of DNA. 3DNALandscapes enables searches of conformational information across multiple structures. The database contains a wide variety of structural param...
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3D-partner
3D-partner is a tool to predict interacting partners and binding models of a query protein sequence through the analysis of structural complexes.
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3D-pssm
Protein fold recognition using 1d and 3d sequence profiles coupled with secondary structure and solvation potential information.
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3DSS
3-Dimensional Structural Superposition (3DSS) is a tool for superposing two or more protein structures that uses RASMOL for visualization; some browser configuration is necessary.
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3Matrix
3Matrix is a tool for visualizing protein sequence motifs and their properties in 3 dimensions. This tool needs to be downloaded and run locally on your own machine.
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3Motif
3Motif is a tool for visualizing protein sequence motifs and their properties in 3 dimensions from PDB structure files.
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3V
The 3V web server extracts and analyzes all of the internal volumes from input RNA and protein structures. Output is volumetric representations in images and downloadable files.
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ACELA
The ACELA (ACcElerated Annotation) tool aims to reduce the human effort required to produce a gold standard corpus of named entity (NE) annotations.
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ACID
The Array Clone Information Database (ACID) is a searchable resource for information about human, mouse, and rat cDNA clones. Each clone contains information about the assigned UniGene cluster(s), location in the full-length ...
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ACLAME
The ACLAME database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids). Classifications are available at various levels of organization. ...
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Acromine
Acromine is an tool that finds full forms of acronyms that appear in MEDLINE.
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Acromine Disambiguator
Given a biomedical text, Acromine Disambiguator correctly predicts expanded full forms of acronoyms appearing in the text. As acronyms appearing in biomedical texts are often ambiguous, such a disambiguation process is import...
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ACT
Arabidopsis Co-expression Tool (ACT) is a resource for investigating the co-expression of genes in the NASC/GARNet microarray-based gene expression dataset from Arabidopsis.
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AD-ENM
Analysis of Dynamics of Elastic Network Model (AD-ENM) predicts the conformational changes a given protein structure can undergo.
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ADGO
ADGO is a web tool that provides composite interpretations for microarray data comparing two sample groups. It also provides composite interpretations and enrichment analysis for lists of genes from diverse sources of biologi...
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Affymetrix NetAffx Analysis Center
Allows correlation of GeneChip array results with array design and annotation information; provides access to array content information, including probe sequences and gene annotations; free registration is required.
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AgBase
AgBase provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. One of seven new tools available a...
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AGenDA
AGenDA is a web tool that compares the genomic sequences from evolutionarily related organisms in order to make gene predictions. It takes pairs of genomic sequences as input, aligns the sequences, and makes predictions based...
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agriGO
agriGO is an integrated gene ontology analysis toolkit for the agriculture community. Supported organisms and gene identifiers were expanded over EasyGO tool, and several tools for predicting gene function are included.
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AGRIS
The Arabidopsis Gene Regulatory Information Server (AGRIS) provides a comprehensive resource for gene regulatory studies in the model plant Arabidopsis thaliana. Three interlinked databases, AtTFDB, AtcisDB and AtRegNet, furn...
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AHD2.0
Arabidopsis Hormone Database (AHD) is a collection of hormone related genes of the model organism Arabidopsis thaliana (AHRGs). AHD2.0 has new features: (i) updating our collection of AHRGs based on most recent publications a...
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AHMII
Agent to Help Microbial Information Integration (AHMII) offers a search engine for particular strains present in culture collections and databases in bacteria, fungi, yeasts and cell lines.
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AIDA
AIDA: Ab Initio Domain Assembly Server attempts to find the best domain arrangements while maintaining chain connectivity. The server also supports structure assembly from sequence only and restraint-guided simulation produci...
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ALADYN
The ALADYN web server aligns pairs of protein structures by comparing their internal dynamics and detecting regions that sustain similar large-scale movements. Input is the structure files of two proteins.
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ALGGEN
ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.
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AlgPred
AlgPred predicts allergenic proteins and maps IgE epitopes on allergenic proteins using several different approaches.
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AliasServer
A tool for converting identifiers in which multiple aliases are used to refer to sequences. Also available as a stand-alone tool.
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AlignACE
Aligns Nucleic Acid Conserved Elements; uses pattern recognition to find elements conserved in a set of DNA sequences; free for non-commercial use with license agreement.
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AlignMe
AlignMe (for Alignment of Membrane Proteins) can be used to examine detailed similarity between homologous proteins even if there is no notable sequence similarity. The predefined gap/weight sets have been optimized for membr...
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Alignment-Annotator
Alignment Annotator is a web service which annotates and renders sequence alignments using annotation services and the PDB. The annotated and colorized alignment can be downloaded as an interactive HTML file for web browsers.
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Alkemio
Alkemio: association of chemicals with biomedical topics by text and data mining
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Allele frequency net
The allele frequency net database is an online repository that contains information on the frequencies of immune genes and their corresponding alleles in different populations. At present, the system contains data on the freq...
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Allen Brain Atlas
The Allen Brain Atlas (ABA) project has developed a web-based application designed to aid the intersection of neuroscience and genomics. The ABA Application enables users to access an extensive database of high resolution in ...
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AltAnalyze
AltAnalyze is a comprehensive tool for the analysis of gene expression and alternative splicing data from RNA-seq and Affymetrix (exon, gene, junction) datasets at the level of proteins, domains, microRNA binding sites and pa...
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ALTER
ALTER is a program-oriented web tool for the conversion between DNA and protein alignments.
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Alternative Splicing Database (ASD) Project
Access to the AltSplice, AltExtron and AEdb databases.
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Alternative Splicing Gallery
The Alternative Splicing Gallery (ASG) takes an identifier such as an EnsEMBL gene ID or a RefSeq ID as input, and provides a graph mapping splice events to transcript information. The user can also view GO information for th...
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Ambion Inc. Technical Resources
Company web site with very good technical resources including an excellent links page, summaries of recent papers on RNA-related topics, and free access to review articles and web features on RNA-related research topics.
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AMIC@
The All Microarray Clustering @ once (AMIC@) web application provides users with a range of microarray gene expression data clustering algorithms. Algorithms can be run concurrently on the same data sets. Data can be visualiz...
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AMIGene
Annotation of MIcrobial Genes (AMIGene) is gene prediction server that can identify coding sequences in microbes.
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The Amino Acid Repository
Includes chemical structures and properties, solvent accessibility, post-translational modifications, and more; with references.
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AmoebaDB and MicrosporidiaDB
AmoebaDB and MicrosporidiaDB are functional genomic databases serving the amoebozoa and microsporidia research communities, respectively. AmoebaDB contains the genomes of three Entamoeba species (E. dispar, E. invadens and E....
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AnalyCys
AnalyCys is database for the analysis of conservation and conformation of disulphide bonds in SCOP structural families. This database has a wide range of applications including mapping of disulphide bond mutation patterns, id...
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ANCHOR
ANCHOR is a web-based tool for the analysis of protein-protein interfaces. ANCHOR indicates possible druggable pockets within the protein using anhor residues.
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Andrej Sali Lab
This page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF).
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ANNIE
ANNIE integrates over twenty protein function prediction tools in a single website. ANNIE displays prediction results in an integrated manner using an innovative AJAX-based sequence viewer.
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AnnotQTL
AnnotQTL is a web tool for gathering functional and comparative information on a genomic region. It is designed to aggregate functional annotations from different websites by minimizing the redundancy of the information.
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AntigenDB
AntigenDB contains 500 antigens to pathogenic species curated from the literature and other immunological resources. In AntigenDB, a database entry contains information regarding the sequence, structure, origin, etc. of an an...
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AntiHunter 2.0
AnitHunter 2.0 is a tool to detect potential EST antisense transcripts within a given genomic region from the analysis of BLAST output.
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antiSMASH
The antibiotic and Secondary Metabolite Analysis Shell (antiSMASH) is a resource for identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.
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APID
Agile Protein Interaction DataAnalyzer (APID) allows you to query protein-protein interactions using a common platform facilitating comparison across different datasets. Currently supported interaction databases are BIND, HPR...
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Apollo Genome Annotation and Curation Tool
Apollo is a genome annotation viewer and editor. Apollo allows researchers to explore genomic annotations at many levels of detail, and to perform expert annotation curation, all in a graphical environment.
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AquaSAXS
AquaSAXS is a web server for computation of and fitting of small angle x-ray scattering (SAXS) profiles with non-uniformally hydrated atomic models.
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Arabidopsis Ensembl
Access to the Arabidopsis thaliana genome through the Ensembl user interface. There are two independent assemblies available, one from TIGR and one from MIPS. Includes the collection of NASC insertion mutants.
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The Arabidopsis Information Resource (TAIR)
Comprehensive resource for the scientific community working with Arabidopsis thaliana.
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ArachnoServer 2.0
ArachnoServer is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. Key features of ArachnoServer include a molecular target ontology des...
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ArchPred
ArchPRED predicts the structure of loop regions in protein structures based on a fragment-search based method. Given a query loop of unknown structure, ArchPRED identifies which loops of know structures are likely to share co...
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AREsite
AREsite is an online resource for the detailed investigation of AU-rich elements (ARE) in vertebrate mRNA 3'-untranslated regions (UTRs). AREsite allows one to quantify the structuredness of ARE motif sites in terms of openin...
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ARGO
ARGO is a tool for the detection and visualization of sets of region-specific degenerate oligonucleotide motifs in the regulatory regions of eukaryotic genes.
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ARISTO
Automatic Reduction of Ion Spectra to Ontology (ARISTO) is a web tool which provides information regarding the chemical nature/ontology of the compound underlying an input electron ionization mass spectrum.
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ArrayExpress
Public repository for microarray based gene expression data; contains several curated gene expression datasets.
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ArrayExpress update
The ArrayExpress Archive is a public repository of functional genomics data supporting publications. It includes data generated by sequencing or array-based technologies. Data are submitted by users and imported directly from...
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ArrayPipe
ArrayPipe allows users to customize a processing pipeline for the analysis of microarray data. Includes methods for quality assessment of slides, data visualization, normalization, and detection of differentially expressed ge...
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ArrayXPath
ArrayXPath is a web-based service for matching microarray gene-expression profiles with known biological pathways. Input is a clustered gene-expression profile in a tab-delimited text format. Output includes pathway diagrams.
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Artemis
DNA sequence viewer and annotation tool; allows visualization of sequence features and results of analyses within the context of the sequence and its 6-frame translation; available for UNIX, Windows and Macintosh.
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ARTS
ARTS (Advanced Retrieval Tool for SNPs) can be used to retrieve SNP that are polymorphic between several different mouse strains to aid in the design of genome-wide SNP marker panels.
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ARTS
Alignment of RNA Tertiary Structures (ARTS) is a method for aligning two nucleic acid structures (RNAs or DNAs) and detecting a-priori unknown common substructures.
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ASAP
ASAP (a systematic annotation package for community analysis of genomes) is a relational database and web interface developed to store, update and distribute genome sequence data and functional characterization. ASAP supports...
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ASD
AlloSteric Database (ASD) provides a central resource for the display, search and analysis of structure, function and related annotation for allosteric molecules. Proteins are annotated with a detailed description of alloster...
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ASePCR
ASePCR (Alternative Splicing electronic PCR) is a tool for carrying out e-PCR to detect differences in amplicon sizes in transcripts from different tissues and organs.
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AsiDesigner
AsiDesigner is a design software system for siRNA design, that takes into account alternative splicing for mRNA level gene silencing. The software also has the capacity to design siRNAs for silencing of multiple mRNAs simulta...
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ASmodeler
Gene modeling server which focuses on the modeling of alternative splicing. It is based on the alignment of mRNA, EST and protein sequences and combines genome-based clustering and transcript assembly. Supports human, mouse a...
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AspGD
The Aspergillus Genome Database (AspGD) is an online genomics resource for researchers studying the genetics and molecular biology of the Aspergilli. AspGD combines high-quality manual curation of the experimental scientific ...
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ASPic
Alternative Splicing Prediction (ASPic) can predict alternative splicing of user submitted genes based on comparative analysis of available transcript and genome data from a variety of species. Results include graphical and t...
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ASPicDB
ASPicDB provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256,939 protein variants from 17,191 multi-exon genes have been extensively annotated through machine learn...
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Assembly PCR Oligo Maker
Assembly PCR Oligo Maker is a tool for designing oligodeoxynucleotides for the PCR based construction of long DNA molecules.
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AStalavista
AStalavista (alternative splicing transcriptional landscape visualization tool) dynamically identifies, extracts, and displays alternative splicing events from whole genome annotations and user provided gene sets.
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Asterias
Asterias is a set of tools for the analyses of high throughput genomic data that includes applications for microarray data normalization, filtering, detection of differential gene expression, class and survival prediction mod...
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AthaMap
AthaMap is a genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana
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ATIVS
ATIVS (analytical tool for influenza virus surveillance) is a web server for analyzing serological data of all influenza viruses and provide interpretive summaries. ATIVS also compares the HA1 sequences of viruses to those of...
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AtPID
The AtPID (Arabidopsis thaliana Protein Interactome Database) represents a centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog informa...
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AUGUSTUS
AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence ...
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AutoClass@IJM
AutoClass is an unsupervised Bayesian classification system. AutoClass@IJM provides a web interface for this clustering algorithm.
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The Autophagy Database
The Autophagy database provides basic, up-to-date information on relevant literature, and a list of autophagy-related proteins and their homologs. From the database, the user can search for proteins by keywords or sequences t...
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AutoSNPdb
SNPServer combines BLAST, cap3 and a SNP discovery module into a single pipeline for the discovery of SNPs in user submitted files or dynamically created assemblies.
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Babelomics
Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and t...
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BAGEL
BActeriocin GEnome mining tooL (BAGEL) identifies putative bacteriocin ORFs (antimicrobial peptides) based on a database containing information about known bacteriocins and adjacent genes involved in bacteriocin activity.
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BAGEL2
BAGEL2 (BActeriocin GEnome mining tooL) identifies putative bacteriocins on the basis of conserved domains, physical properties and genomic context. Improved genome mining capacity from BAGEL.
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BAGET
BAGET (Bacterial and Archaeal Gene Exploration Tool) is a web service designed to facilitate extraction of specific gene and protein sequences from completely determined prokaryotic genomes. Query results can be exported as a...
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BankIt
Web-based submission of one or a few sequences to GenBank.
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BAR-PLUS
BAR-PLUS is a web tool for functional and structural annotation of protein sequences based on a large scale genome cross comparison and a non-hierarchical clustering procedure. Sequence annotation is derived from UniProtKB, G...
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BASys
BASys (Bacterial Annotation System) is a tool for automated annotation of bacterial genomic (chromosomal and plasmid) sequences including gene/protein names, GO functions, COG functions, possible paralogues and orthologues, m...
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BCHIMPS
BC Health Information Management Professionals' Society (BCHIMPS) non-profit organization that is responsible for managing health information within BC.
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BCM Search Launcher
Molecular biology-related search and analysis services organized by function; single point-of-entry for related searches (e.g., a single page for launching protein sequence searches using standard parameters).
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BCM Search Launcher Sequence Utilities
Includes reverse complement, 6-frame translation, RepeatMasker, ReadSeq format conversion.
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BEARR
Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of m...
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BeeSpace Navigator
BeeSpace Navigator is a tool for exploratory analysis of gene function using biological literature. It is an automated version of the curation process to extract gene function.
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BeetleBase
BeetleBase (http://www.beetlebase.org) has been updated to provide more comprehensive genomic information for the red flour beetle Tribolium castaneum. The database contains genomic sequence scaffolds mapped to 10 linkage gro...
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Berkeley Drosophila Genome Project
Good entrez to fly genome resources.
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Berkeley Phylogenomics Group
The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clu...
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Bgee
Bgee is a dataBase for Gene Expression Evolution. It allows one to automatically compare gene expression patterns between species, by referencing expression data on anatomical ontologies, and designing homology relationships ...
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BhairPred
BhairPred is a tool for predicting beta-hairpins in protein sequences using a support vector machine.
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BiERapp
BierApp is a web-based interactive framework to assist in the prioritization of disease candidate genes in whole exome sequencing studies.
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BindN
BindN takes an amino acid sequence as input and predicts potential DNA or RNA-binding residues using support vector machines (SVMs).
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BIND SOAP
BIND SOAP is a web service providing end users with the ability to access functionality offered by the BIND Search Service through a remote Application Programming Interface (API).
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BIND - The Biomolecular Interaction Network Database
Stores full descriptions of interactions, molecular complexes and pathways; researchers are able to submit new records.
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BIOBASE Gene Regulation databases
includes: TRANSFAC - transcription factor database; Patho DB - mutated forms of transcription factors and binding sites that are pathologically relevant; S/MARt DB - scaffold matrix transaction database; TRANSPATH - gene regu...
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BioBayesNet
BioBayesNet is a server for feature extraction and Bayesian network modeling of biological sequence data.
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BioBIKE
BioBIKE is a web-based environment enabling biologists with little programming expertise to combine tools, data and knowledge in novel and complex ways. BioBIKE is composed of three components: a biological knowledge base, a ...
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BioCarta
Information about gene function, proteomic pathways, and reagent exchange; very clear pathway diagrams; can search for pathways by title or browse an organized list.
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BioCatalogue
A universal catalogue of web services for the life sciences. BioCatalogue provides a common interface for registering, browsing and annotating web services to the life science community.
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Bioconductor
Bioconductor is an open source and open development software project that aims to provide access to a wide range of powerful statistical and graphical methods for the analysis of genomic data.
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BioCyc Knowledge Library
BioCyc is a collection of pathway/genome databases derived either from the literature (EcoCyc and MetaCyc) or computationally (ie. HumanCyc). EcoCyc is used to visualize gene layout, biochemical reactions, and pathways for th...
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BioDAS
This site is the center of development of an Open Source system for exchanging annotations on genomic sequence data.
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BioDBcore
BioDBCore is a community-defined, uniform, generic description of the core attributes of biological databases.
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BioDrugScreen
BioDrugScreen is a resource for ranking molecules docked against a large number of targets in the human proteome. Nearly 1600 molecules from the freely available NCI diversity set were docked onto 1926 cavities identified on ...
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BioExtract
The BioExtract Server is a platform for the creation of bioinformatic workflows to aid the analysis of genomic data. A series of recorded tasks can be saved and shared. Integrated resources include NCBI databases, EMBL-Bank, ...
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The BioGRID Interaction Database
The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans. Complete coverage of the entire li...
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BioInfo3D
BioInfo3D is a collection of tools for the structural analysis of proteins, including tools for structural alignments and prediction of protein interactions.
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Bioinformatics Links Directory
The Bioinformatics Links Directory features curated links to molecular resources, tools and databases. All of the resources are free or available for a nominal fee.
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The Bioinformatics Organization, Inc.
Bioinformatics.org was founded to facilitate interaction between established and aspiring bioinformatics researchers. The website provides many resources, including project hosting, online databases and analysis tools, and se...
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Bioinformatics Toolkit
This Toolkit is a collection of a wide range of tools and links for sequence analysis, function, and structure prediction. This resource offers convienent web interfaces for many freely available tools.
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Bioinformatik
Yahoo-like Webdirectory for bioinformatics.
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Bio-IT World
BIO IT technology trends & forecasts, industry news & analysis, bioinformatics and drug discovery updates.
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BioJava
The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.
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BIOKNOPPIX
BIOKNOPPIX is a live distribution of the Linux operating system that can be run from a CD drive (see also KNOPPIX). BIOKNOPPIX is loaded with bioinformatics applications.
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Bio-Linux
A bioinformatics-centric distribution based on Ubuntu LTS, with a public repository of pre-compiled bioinformatics packages in DEB format. Over 100 packages including BLAST+, EMBOSS, Qiime, Mothur, Ampliconnoise.
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BioLit
BioLit is a web sever resource that integrates scientific publications with existing biological databases. To perform this link, BioLit searches the full text of the article for metadata such as database identifiers and ontol...
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BiologicalNetworks
BiologicalNetworks allows retrieval, construction, and visualization of biological networks and allows for the analysis of high-throughput expression data by mapping onto network graphs. BiologicalNetworks queries the PathSys...
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Biology Online
Biology-Online.org is a free resource for biology related information in forms of tutorials, articles, dictionary and forums. Discussion and information sharing about various topics in biology and related disciplines occur.
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BioMart
BioMart is an interactive data integration system facilitating large-scale data queries. It can be installed and used in-house, or with one of the existing data sources to which is has already been applied (ie. UniProt, Ensem...
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BioMet Toolbox
The BioMet Toolbox consists of web-based resources for stoichiometric analysis of metabolic networks and for integration of transcriptome and interactome data into these networks to simulate growth rates, substrate uptake rat...
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BioMet Toolbox 2.0
BioMet Toolbox 2.0 is a web server for genome-wide analysis of metabolism and omics data. BioMet Toolbox exploits the capabilites of metabolic networks described in genome scale models using flux analysis and random sampling,...
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BioMoby
BioMOBY is an international research project involving biological data hosts, biological data service providers, and coders whose aim is to explore various methodologies for biological data representation, distribution, and d...
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bioNMF
A web-based tool based on nonnegative matrix factorization (NMF) that can be used to provide new information from multi-dimensional biological data sets.
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BioNumbers
BioNumbers (http://www.bionumbers.hms.harvard.edu) is a database of key numbers in molecular and cell biology--the quantitative properties of biological systems of interest to computational, systems and molecular cell biologi...
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BioPax
The BioPAX web site provides information about a collaborative effort to create a data exchange format for biological pathways.
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BioPerl
The BioPerl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research.
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BioPerl course
Great tutorial for those interested in the bioperl group of modules.
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BioPHP
Open Source PHP code for bioinformatics. Includes functions and minitools (copy and paste one page scripts for basic tasks in bioinformatics. A wiki-like service allows modification and improvement of code.
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BioPortal
BioPortal is a web accessible open repository of biomedical ontologies. Users may browse, search and visualize ontologies, as well as participate in the evaluation and evolution of ontology reviews by adding notes, correction...
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BioProfiling.de
BioProfiling.de provides a toolkit for the interpretation of gene or protein lists using enrichment of network based statistical frameworks.
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BioProspector
Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predic...
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BioPython
The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
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BioRuby
The BioRuby project aims to implement an integrated environment for bioinformatics with Ruby.
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BioSystems
The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allo...
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BioTeach
Great articles on all sorts of biological topics including bioinformatics.
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Bioverse
Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.
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BiQ Analyzer HiMod
BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives
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BiQ Analyzer HT
BiQ Analyzer HT Is a tool that supports locus specific analysis and visualization of high-throughput bisulfite sequencing data. It facilitates analysis of locus specific DNA methylation patterns.
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BISC
Binary subcomplexes in proteins database (BISC) is a protein-protein interaction (PPI) database linking up the two communities most active in their characterization: structural biology and functional genomics researchers. The...
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BLAST
Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches....
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Blast2GO
The Blast2GO suite is a comprehensive bioinformatics tool for functional annotation of plant sequences and data mining on the resulting annotations, primarily based on the gene ontology (GO) vocabulary. The application suppor...
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BLAST2SRS
BLAST2SRS (Sequence Retrieval System) is a tool to retrieve protein sequences using similarity (BLAST) and keyword searches.
website       summary

BLASTO
BLASTO (BLAST on Orthologous groups) is a modified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences.
website       summary

Blocks WWW Server
The Blocks WWW server provides tools to search DNA and protein queries against the Blocks database of multiple alignments, which represent conserved protein regions.
website       summary

BOMP
The beta-barrel Outer Membrane protein Predictor (BOMP) takes one or more fasta-formatted polypeptide sequences from Gram-negative bacteria as input and predicts whether or not they are beta-barrel integral outer membrane pro...
website       summary

botXminer
botXminer is a literature searching tool that allows you to search BotDB. BotDB citations contain only those articles with either \'botulinum\' or \'tetanus\' anywhere in their text. botXminer is an interface to this subset o...
website       summary

Bovine Genome Database
The Bovine Genome Database (BGD) includes mechanisms too improve annotation of the bovine genome and to integrate the genome sequence with other genomics data. BGD includes GBrowse genome browsers, the Apollo Annotation Edito...
website       summary

BoxShade
Printing and shading of multiple alignment files.
website       summary

BRENDA
The BRENDA (BRaunschweig ENzyme Database) enzyme information system is a collection of enzyme functional and property data, manually extracted from the primary literature. The content covers information on function, structure...
website       summary

BRENDA - The Comprehensive Enzyme Information System
Information about reaction and specificity, post-translational modifications, structure, stability, and references to other databases; free for academics.
website       summary

The BRENDA Tissue Ontology (BTO)
BTO, the BRENDA Tissue Ontology is a structured encyclopedia of tissue terms. BTO contains different anatomical structures, tissues, cell types and cell lines, classified under generic categories corresponding to the rules an...
website       summary

BriX
BriX is a vast database of protein fragments, clustered on their backbone similarity. BriX contains fragments from 7290 proteins from the Astral40 set, fragmented in lengths ranging from 4 to 14 amino acids and clustered agai...
website       summary

BROP
The Bioinformatics Resource for Oral Pathogens (BROP) contains tools for genomics of oral pathogens including Genome Viewer, GOAL (genome wide ORF alignment), an oral pathogen microarray database, an entrez counter, oral path...
website       summary

BSDB
The Biomolecule Stretching Data provides information about mechanostability of proteins. Its core is based on simulations of stretching of proteins within a structure-based model. The primary information is about the heights ...
website       summary

BSDD
BSDD (Biomolecules Segment Display Device) searches for and displays user defined sequence motifs in known protein structures. This web based tool incorporates the graphics package of RASMOL for visualization.
website       summary

BSQA
BeeSpace Question/Answering (BSQA) system is a web server that performs integrated text mining for insect biology, covering diverse aspects from molecular interactions of genes to insect behavior. BSQA recognizes a number of ...
website       summary

BTW
Boltzmann Time Warping (BTW) computes time warping distances and Boltzmann\' pair probabilities for a given input gene expression time series. This tool helps to identify genes that may share similar expression patterns over ...
website       summary

Build your own arrayer
The MGuide (version 2.0). The Brown Labs complete guide to microarraying for the molecular biologist.
website       summary

caBIO Web Services
SOAP interfaces used to access the cancer Bioinformatics Infrastructure Objects(caBIO) funtionality.
website       summary

CAD-score
The CAD-score web server provides a contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes.
website       summary

CADgene
The CADgene, a comprehensive manually curated database for coronary artery disease genes. Candidate genes are classified into 12 functional categories based on their roles in CAD. Each gene includes detailed information from ...
website       summary

CAMERA
The Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA) is a database and associated computational infrastructure that provides a single system for depositing, locating, analyzing, visu...
website       summary

CAMP
Collection of Anti-Microbial Peptides (CAMP) is a free online database that is manually curated and currently holds 3782 antimicrobial sequences. These sequences are divided into experimentally validated (patents and non-pate...
website       summary

CAMPO
CAMPO is a tool to analyze conserved regions from a multiple sequence alignment
website       summary

Canada Bioinformatics People
Principal investigators and group leaders from academia, government labs, and industry with an interest in development of bioinformatics resources in Canada.
website       summary

Canada Health Infoway
Canada Health Infoway is working to develop a network of electronic health records across Canada in order to improve the quality and access to healthcare services, therefore making them more productive.
website       summary

Canadian Bioinformatics Workshops
Hands-on instruction in the use and development of software tools for genomic and computational biology research.
website       summary

Canadian Microarray Resources
Contact information, availabilities and expertise of Canadian microarray centres; includes labs that supply cDNA or oligonucleotide spotted arrays and other services, and labs that can analyse RNA with Affymetrix chips.
website       summary

Canadian Society for Systems Biology
The Canadian Society for Systems Biology aims at supporting and developing initiatives that strengthen Systems Biology research in Canada.
website       summary

Cancer Genome Anatomy Project
Goal is to determine the gene expression profiles of normal, precancer, and cancer cells; resources for human and mouse include ESTs, gene expression patterns, SNPs, cluster assemblies, cytogenetic information, and tools to q...
website       summary

CancerResource
CancerResource, a database that integrates cancer-relevant relationships of compounds and targets from (i) literature mining and (ii) external resources complemented with (iii) essential experimental and supporting informatio...
website       summary

Candida Genome Database
The Candida Genome Database provides online access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. Two tools have been added to the DB. The...
website       summary

CanPredict
CanPredict uses a combination of computational methods to predict whether specific sequence changes in a protein are likely to be cancer-associated mutations.
website       summary

CAP3 Sequence Assembly Program
Web-based contig assembly.
website       summary

CAPweb
CGH array Analysis Platform (CAPweb) is a tool for storing, analyzing and visualizing CGH-array data.
website       summary

CARGO
CARGO (Cancer And Related Genes Online) is a portal that uses widgets to allow users to mine literature using iHOP, retrieve disease information from OMIM, visualize 3D SNPs, query protein interactions, and view summarized ge...
website       summary

CARMAweb
Comprehensive R based Microarray Analysis web service (CARMAweb) is a resource for the analyses of microarray data including data preprocessing, detection for differentially expressed genes, cluster analysis, and GO analysis....
website       summary

CARNAC
Server which predicts conserved secondary structure elements of homologous RNAs. The input of a set of RNA sequences are not required to be previously aligned.
website       summary

CARRIE
Server which analyzes microarray and promoter sequence data associated with a response to a specific stimulus. After analysis a potential transcriptional regulatory network is created. CARRIE also determines which transcripti...
website       summary

Cascade PSI-Blast
Cascade PSI-BLAST detects distant protein similarities using a cascade search protocol where PSI-BLAST searches are carried out on each hit, until no new hits are found in the selected database (SwissProt, SCOP, or Pfam).
website       summary

CaSNP
CaSNP database for storing and interrogating quantitative copy number alterations (CNA) data from SNP arrays on 34 different cancer types in 104 studies. With a user input of region or gene of interest, CaSNP will return the ...
website       summary

CaspR
CaspR is a web tool for building structural models for protein sequences using molecular replacement and homology modelling. The software implements an automated approach that uses T-COFFEE to produce alignments, MODELLER to ...
website       summary

CASTp
Computed Atlas of Surface Topography of proteins (CASTp) locates and measures concave surface regions on 3D protein structures. This tool can be used to study surface features, binding sites, and functional regions of protein...
website       summary

The catfish genome database cBARBEL
The catfish genome database, cBARBEL (abbreviated from catfish Breeder And Researcher Bioinformatics Entry Location) is an online open-access database for genome biology of ictalurid catfish (Ictalurus spp.). cBARBEL provides...
website       summary

CATH
Database of automated protein structure classification according to Class (C), Architecture (A), Topology (T) and Homologous superfamily (H).
website       summary

CATH
CATH is a manually curated classification of protein domain structures. Each protein has been chopped into structural domains and assigned into homologous superfamilies (groups of domains that are related by evolution). This ...
website       summary

CBS DAS protein viewer
The CBS DAS protein viewer uses the distributed annotation system (DAS) to integrate and present annotation data from multiple sources for a protein sequence.
website       summary

CCancer
CCancer is an automatically collected database of gene lists reported in various studies. The current coverage is 3369 gene lists from 2644 papers. Enrichment analysis reports intersecting gene lists with an inputted gene lis...
website       summary

CCDB
The Cervical Cancer gene DataBase (CCDB) is a manually curated catalog of experimentally validated genes that are thought, or are known to be involved in the different stages of cervical carcinogenesis. Each record contains d...
website       summary

CCRXP
A tool for the detection of conserved residue clusters from an input PDB file. Structural properties of each residue, such as solvent accessibility (ASA), secondary structure, conservation score etc. and the conserved residue...
website       summary

CCT
CCT (Current Comparative Table) is a software package that you can install and set-up on your own system to help you to maintain and search databases.
website       summary

CDD
NCBI's Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. CDD includes manually curated...
website       summary

CDDB
The conformational dynamics data bank (CDDB) is a database for comprehensive results on the conformational dynamics of high molecular weight proteins and protein assemblies. Analysis is performed using a coarse-grained comput...
website       summary

CD-Search
CD-Search allows the user to search the Conserved Domain Database (CDD) for conserved structural and functional domains in a sequence of interest; links to 3-D structures where applicable.
website       summary

CEAS
Cis-regulatory Element Annotation System (CEAS) is a resource for ChIP-chip analyses that retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes, and identifies en...
website       summary

C. elegans Gene Knockout Consortium
Worldwide consortium whose ultimate goal is to produce null alleles of all known genes in the C. elegans genome; submit your gene to the knockout list.
website       summary

CE-MC
A multiple protein structure alignment server which creates an all-to-all pairwise alignment using a combinatorial extension program and then using Monte Carlo optimization methods conducts an iterative global optimization. R...
website       summary

CENTDIST
CENTDIST is a co-motif scanning program to identify co-transcription factors. CENTDIST ranks co-transcription factors based on their distribution around CHIP-seq peaks.
website       summary

Center for Law and Genetics
Contains numerous articles concerning the legal and ethical issues arising from the developments in genetic technology.
website       summary

CentroidFold
Recognizing the growing role for non-coding RNAs (ncRNAs) in cells, the CentroidFold web server predicts RNA secondary structure from input sequence data (single or multiple alignments).
website       summary

CentroidHomfold-LAST
CentroidHomfold-LAST predicts the secondary structure of an RNA sequence using automatically collected homologous sequences.
website       summary

CFM-ID
CFM-ID (Competitive Fragmentation Modeling) is a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra data.
website       summary

CGView Server
The CGView Server generates graphical maps of circular genomes that can be used to visualize sequence conservation in the context of sequence features, imported analysis results, open reading frames and base composition plots...
website       summary

CHAOS/DIALIGN WWW server
The CHAOS/DIALIGN WWW server is a multiple sequence alignment site which passes input sequences through CHAOS to create a list of local similarites. These similarities serve as anchor points, allowing DIALIGN to conduct globa...
website       summary

CHC_FIND
CHC_FIND is a tool to analyze conserved hydrophobic contacts (CHC) from multiple structural alignments. In addition to a multiple sequence alignment, a structural alignment which provides the superposition of structurally con...
website       summary

ChEBI
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. The molecular entities in question are either natural products or synthetic produc...
website       summary

ChemMine Tools
ChemMine Tools is an online service for analyzing and clustering small molecules. A suite of cheminformatics and data mining tools for data visualization, structure comparison, similarity searching, compound clustering and pr...
website       summary

ChemProt
ChemProt, a disease chemical biology database, which is based on a compilation of multiple chemical-protein annotation resources, as well as disease-associated protein-protein interactions (PPIs). The PPI network layer allows...
website       summary

ChemSynthesis
ChemSynthesis is a freely accessible database of chemicals. This website contains substances with their synthesis references and physical properties such as melting point, boiling point and density. Over 40,000 compounds are ...
website       summary

Chilibot
Chilibot searches the PubMed literature database based on specific relationships between proteins, genes, or keywords. The results are returned as a graph.
website       summary

CHIMA
The Canadian Health Information Management Association (CHIMA) is a membership-based organization that manage the security, privacy and accuracy of patient records in hospitals across Canada.
website       summary

ChimerDB
ChimerDB is a knowledgebase of fusion genes identified from bioinformatics analysis of transcript sequences in the GenBank and various other public resources such as the Sanger cancer genome project (CGP), OMIM, PubMed and th...
website       summary

Chinook
Chinook is a peer-to-peer (P2P) service for the discovery, use and assessment of bioinformatics programs. Chinook Online allows researchers to connect and run distributed bioinformatics programs using a web application.
website       summary

ChIP-Array
ChIP-Array is a web server that integrates ChIP-seq and microarray gene expression data to discover direct and indirect target genes regulated by a transcription factor of interest.
website       summary

chipD
chipD is a web server that facilitates the design of DNA oligonucleotide probes for high-density tiling arrays. The algorithm ensures probe specificity, thermodynamic properties amongst probe sets and target sequence coverage...
website       summary

ChipInfo
ChipInfo extracts gene annotation and gene ontology information from databases like NetAffx and Gene Ontology (GO) for microarray analysis. Output is provided in tabular format and the program is available for download for us...
website       summary

CHOP
CHOP takes a protein sequence as input, and returns a list of protein sequence fragments with homology to PDB and Pfam domains and to proteins from the SWISS-PROT database.
website       summary

CHOPCHOP
CHOPCHOP is a web tool for selecting the optimum target sites for CRISPR/Cas9- or TALEN-directed mutagenesis. It can be run with three basic input options, or with additional advanced parameters. The basic input comprises: (i...
website       summary

The Chromosome 7 Annotation Project
The Chromosome 7 database is a community-curated project which contains the most up to date collation of sequence, gene, and other annotations from all databases (eg. Celera published, NCBI, Ensembl, RIKEN, UCSC) as well as u...
website       summary

CIBEX
The Center for Information Biology gene EXpression database (CIBEX) is a public repository for gene expression experimental data. The database system is compliant with the MIAME standard.
website       summary

CiF
The Cyber infrastructure for Fusarium (CiF) consists of Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP) and Fusarium Community Platform (FCP). The Fusarium-ID archives phylogenetic marker sequences from most known ...
website       summary

CIPRes
The Cyberinfrastructure for Phylogenetic Research (CIPRes) project aims to develop a computational infrastructure for systematics. Other goals of the project include providing a central resource enabling computational systema...
website       summary

CIPRO 2.5
The Ciona intestinalis protein database (CIPRO) is an integrated protein database for the tunicate species C. intestinalis. The CIPRO database collects published data as well as unique information from unpublished experimenta...
website       summary

CisMols
CisMols (Cis-regulatory Modules) is a tool that identifies compositionally predicted cis-clusters that occur in groups of co-regulated genes within each of their ortholog-pair evolutionarily conserved cis-regulatory regions.
website       summary

cisRED
cisRED is a database system for genome-scale computational discovery of regulatory elements.
website       summary

ClanTox
ClanTox, a classifier of short animal toxins, predicts whether input sequences are toxin-like based on classification system training to known animal toxins. This dscovery prediction tool also outputs presence of signal pepti...
website       summary

CLIC
CLIC performs clustering analysis of large microarray datasets. Genes are first clustered in individual dimensions and then using the ordinal labels of clusters for each dimension, full dimension wide clustering is performed.
website       summary

CLICK
CLICK web server is a topology independent method of comparison of biomolecular 3D structures.
website       summary

CLIP
CLIP web server detects selection in immunoglobulin sequences. Web server features include V(D)J germline segment identification with IMGT-alignment, batch submission of sequences and integration of test statistics.
website       summary

CLIPZ
CLIPZ supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of ...
website       summary

ClusPro
ClusPro is a tool for automatically computing the docking of two protein structures supplied by the user (or as PDB IDs). The result set is a ranked list of putative complexes, ordered by clustering properties.
website       summary

ClustalW
Standard multiple sequence alignment.
website       summary

ClustalX
Clustal X is a version of the Clustal W multiple sequence alignment program with a graphical interface. The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for sev...
website       summary

Cluster Buster
Cluster Buster is a tool that finds clusters of pre-specified motifs in DNA sequences.
website       summary

CMA
Composite Module Analyst (CMA) defines promoter models based on the composition of transcription factor binding sites (TFBS) in regulatory sequences for sets of coregulated genes.
website       summary

CMR
The Comprehensive Microbial Resource (CMR) gives access to a central repository of the sequence and annotation of all complete public prokaryotic genomes as well as comparative genomics tools across all of the genomes in the ...
website       summary

CMS Molecular Biology Resource
Compendium of electronic and Internet-accessible tools and resources for Molecular Biology, Biotechnology, Molecular Evolution, Biochemistry and Biomolecular Modeling.
website       summary

Cn3D
Web browser helper application that simultaneously displays 3-D structure, sequence, and alignment.
website       summary

COACH
Canadian Organzation for the Advancement of Computers in Health (COACH) is an organization that promotes understanding of health informatics within the Canadian health system through education, information, networking and com...
website       summary

CODEHOP
COnsensus-DEgenerate Hybrid Oligonucleotide Primers (CODEHOP); degenerate PCR primer design; will accept unaligned sequences.
website       summary

CodonO
CodonO is a method for measuring synonymous codon usage bias within and across genomes.
website       summary

Codon Usage Database
Find GC content and frequency of codon usage for any organism that has a sequence in GenBank.
website       summary

COGNAC
COGNAC: a webserver for searching and annotating hydrogen bonded base interactions in RNA 3-dimensional structures.
website       summary

COGs
Clusters of Orthologous Groups represent ancient conserved protein domains; use COGnitor tool to find COGS in sequence of interest.
website       summary

COILS
Prediction of coiled coil regions.
website       summary

COLORADO-3D
COLORADO-3D allows you to color your protein structures to indicate the presence of potential errors in protein structure (detected by ANOLEA, PROSAII, PROVE or VERIFY3D), buried residues, and sequence conservation. The serve...
website       summary

Color Base Pair
On-line bioinformatics resources including links to news, forums, tutorials, and jobs.
website       summary

COMA
COMA is a distant homology detection method based on sequence profile–profile comparison. COMA takes a protein sequence or multiple sequence alignment as input and searches for remote homologs in SCOP, PDB and PFAM database...
website       summary

Combinatorial Extension of the Optimal Path
Calculates structural alignments between two protein chains; or between a single chain and the entire Protein Data Bank.
website       summary

COMBREX
COMBREX is a project to increase the speed of the functional annotation of new bacterial and archaeal genomes. It consists of a database of functional predictions produced by computational biologists and a mechanism for exper...
website       summary

CoMet
CoMet is a web server for comparative metagenomics, and is particularly suited for analysis of large collections of metagenomic short read data.
website       summary

The Comparative Toxicogenomics Database
The Comparative Toxicogenomics Database (CTD) is a curated database about the interaction of environmental chemicals with gene products, and their effects on human health. New features include statistical analyses and analyti...
website       summary

CompareProspector
Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species.
website       summary

COMPASS
COMPASS (Comparison of Multiple Protein Alignments with Assessment of Statistical Significance) is a tool for detecting remote levels of sequence similarity using profile-based comparison of multiple sequence alignments. Stat...
website       summary

Comprehensive Microbial Resource (CMR)
The Comprehensive Microbial Resource provides a web-based central resource for the display, search and analysis of the sequence and annotation for complete and publicly available bacterial and archaeal genomes. In addition to...
website       summary

ComSin
ComSin is a database of protein structures in bound (complex) and unbound (single) states. The developed server enables one to search for proteins in bound and unbound states with several options including sequence similarity...
website       summary

CONFAC
The Conserved Transcription Factor Binding Site Finder (CONFAC) takes a list of human gene names and identifiers as input, and compares them with their mouse orthologues to identify conserved transcription factor binding site...
website       summary

ConPlex
ConPlex is a web server that enables conservation analyses of protein interactions within protein quaternary structures. Results of the residue specific conservation analysis are displayed on the input protein complex structu...
website       summary

CONREAL
CONREAL (Conserved Regulatory Elements Anchored Alignment) allows identification of transcription factor binding sites (TFBS) that are conserved between two orthologous promoter sequences.
website       summary

ConsensusPathDB
ConsensusPathDB is a meta-database that integrates physical protein interactions, metabolic and signaling reactions and gene regulatory interactions in a seamless functional association network that simultaneously describes m...
website       summary

ConSeq
ConSeq is a tool for predicting functionally and structurally important amino acid residues in protein sequences. The predictions are based on the assumptions that residues of functional importance are often conserved and sol...
website       summary

Consite
Detect transcription factor binding sites in genomic sequences using phylogenetic footprinting and experimentally-confirmed binding profiles.
website       summary

ConSurf
The ConSurf server allows one to map levels of amino acid conservation to known protein structures in order to study areas of potential functional importance on the surface of the protein. A PDB file is required as input, and...
website       summary

ConTra
The Conserved Transcription Factor Binding Sites (ConTra) is a promoter alignment analysis tool to identify transcription factor binding sites across species. This web server allows users to interactively visualize transcript...
website       summary

CopraRNA and IntaRNA
CopraRNA and IntaRNA webserver tools: CopraRNA is a tool for sRNA target prediction, while IntaRNA enables the prediction of RNA-RNA interactions.
website       summary

COPS
The Classification of Protein Structures (COPS) web server is a workbench for visualizing and examining proteins in fold space. Access is given to all known protein structures and protein structural domains. Structures and do...
website       summary

CoPub
CoPub is a text mining tool for the detection of biomedical terms that co-occur in abstracts with the list of input genes (human, rat, and mouse genes). CoPub also graphically displays differentially expressed genes and over-...
website       summary

CorGen
CorGenmeasures long-range correlations in DNA sequences and can generate random sequences with the same (or user-specified) correlation and composition parameters.
website       summary

CorreLogo
CorreLogo generates a 3D sequence logo for RNA or DNA alignments. The first two dimensions of the sequence logo display information about the information content and residue composition of individual columns of the alignment....
website       summary

corRna
corRna is a web server for predicting the multiple point deleterious mutations in structural RNAs. Users can apply search heuristics to improve the quality of the predictions.
website       summary

CORUM
CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (64%), mouse (16%) and rat (12%). The CORUM dataset is built from 3198 d...
website       summary

COSMIC
COSMIC curates comprehensive information on somatic mutations in human cancer. Release v48 (July 2010) describes over 136,000 coding mutations in almost 542,000 tumour samples; of the 18,490 genes documented, 4803 (26%) have ...
website       summary

COUGER
COUGER - CO-factors associated with Uniquely-bound GEnomic Regions. This webserver can be applied to any two sets of genomic regions bound by paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify putati...
website       summary

COXPRESdb
COXPRESdb (coexpressed gene database) represents the coexpression relationship for human and mouse. Upgrades include a new comparable coexpression measure, Mutual Rank, five other animal species, rat, chicken, zebrafish, fly ...
website       summary

CPA - Comparative Pathway Analyzer
The Comparative Pathway Analyzer (CPA) is a web tool for comparative metabolic network analysis. The differences in metabolic reaction content between two sets of organisms are computed and displayed on KEGG pathway maps.
website       summary

CPC
CPC (Coding Potential Calculator) distinguishes protein-coding from non-coding RNAs based on the sequence features of the input transcripts.
website       summary

CPHmodels-3.0
CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling.
website       summary

CPLA 1.0
Compendium of protein lysine acetylation (CPLA) database is a resource of manually curated lysine acetylated substrates with their sites.
website       summary

cpnDB
cpnDB is a curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The dat...
website       summary

Cprogramming.com
Cprogramming.com is a web site designed to help you learn C or C++ and provide you with C and C++ programming resources.
website       summary

CRASP
Correlation analysis of the amino acid substitutions in protein sequences (CRASP) takes multiple alignments of amino acid sequences as input, and detects coordinated residue substitutions. These substitutions may suggest depe...
website       summary

CREME
CREME (Cis-Regulatory Module Explorer for the human genome) is a tool for identifying and visualizing cis-regulatory modules for a given set of genes that are potentially co-expressed or co-regulated. It takes as input a list...
website       summary

CRISPRcompar
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) elements are used in CRISPRcompar as a genetic marker for comparative and evolutionary analysis of closely related bacterial strains.
website       summary

CRISPRFinder
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Finder detects this family of direct repeats found in the DNA of many bacteria and archaea.
website       summary

CrossLink
Crosslink is a tool for visualizing pairwise sequence similiarity relationships determined using BLAST, Vmatch, and RNAhybrid. The nucleotide sequences and their relationships are displayed as nodes and links of a network, re...
website       summary

CRP
Cleaved Radioactivity of Phosphopeptides (CRP) performs in silico proteolytic cleavage of protein sequences and reports the radioactivity that would be observed if a given serine, threonine or tyrosine were phosphorylated.
website       summary

CRSD
Composite Regulatory Signature Database (CRSD) is a microarray analysis pipeline aimed at the discovery of motifs involved in gene regulation including microRNA signatures and transcription factor binding sites (TFBS).
website       summary

CS23D
Chemical Shift to 3D Structure (CS23D) generates accurate 3D protein structures using only NMR chemical shifts and sequence data. Output is a set of PDB coordinates for the protein.
website       summary

CSHL Oral History Collection
A collection of oral histories through the eyes of more than fifty scientists who have worked at and visited Cold Spring Harbor Laboratory. Provides a great perspective on the early years of molecular biology and visions of t...
website       summary

CSpritz
CSpritz is a web server for the prediction of intrinsic protein disorder segments with annotation for homology, secondary structure and linear motifs.
website       summary

CSTminer
CSTminer searches for Conserved Sequence Tags (CST) in pairwise comparisons of genomic sequences. Output is a graphical map showing the location of CSTs overlayed with known Ensembl exons and ESTs. A scoring system reflects c...
website       summary

CUPSAT
Cologne University Protein Stability Analysis Tool (CUPSAT) is a tool to analyse and predict protein stability changes upon point mutations (single amino acid mutations) for known protein structures.
website       summary

CURVES+
Curves+ is a web server for the analysis and visualization of the helical backbone and groove parameters of nucleic acid structures.
website       summary

CVTree
Composition Vector Tree (CVTree) infers phylogenetic relationships between microbial organisms by comparing their proteomes using a composition vector approach.
website       summary

CyanoBase
CyanoBase is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information, complete genome sequences, genome-scale experiment data, gene informatio...
website       summary

Cyclebase
Cyclebase is an online resource of cell-cycle-related experiments. This database provides an easy-to-use web interface that facilitates visualization and download of genome-wide cell-cycle data and analysis results. Data from...
website       summary

CyloFold
CyloFold is a web tool for RNA secondary structure prediction that is not restricted in terms of pseudoknot complexity.
website       summary

Cytoscape
Cytoscape is a visualization platform for use with molecular interaction networks. Interaction data can be integrated with other state data such as gene expression profiles. The input to Cytoscape includes lists of interactio...
website       summary

Dali server
The Dali server compares newly solved structures against structures in the PDB, allows browsing of pre-computed structural neighborhoods and generates suboptimal alignments from pairwise structure comparisons.
website       summary

DAnCER
The DAnCER (Disease Annotated Chromatin Epigenetic Resource) resource integrates information on genes with chromatin modification (CM) function from five model organisms, including human. Currently integrated are gene functio...
website       summary

Daphnia Genomics Consortium
The Daphnia Genomics Consortium (DGC) is an international network of investigators committed to mounting the freshwater crustacean Daphnia as a model system for evolutionary / ecological genetics and genomics.
website       summary

DARIO
DARIO is a web service for the study of short read data from small RNA-seq experiments. It provides a wide range of analysis features including qulity control, read normalization, ncRNA quantification and prediction of putati...
website       summary

DASMIweb
The DASMIweb server allows integration, analysis and quantitative assessment of distributed sources of protein and domain interactions. Users can query numerous sources simultaneously, which can then be configured and can sup...
website       summary

DATF
The Database of Arabidopsis Transcription Factors (DATF) contains information of more than 1800 known and predicted transcription factors for Arabidopsis.
website       summary

DAVID Bioinformatics Resources
The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.
website       summary

DBAli
DBAli is a database that includes a comprehensive all-against-all comparison of protein structures in the PDB database. Tools associated with the database allow users to mine this protein structure space by establishing relat...
website       summary

DBASS3 and DBASS5
DBASS3 and DBASS5 provide comprehensive repositories of new exon boundaries that were induced by pathogenic mutations in human disease genes. Aberrant 5'- and 3'-splice sites were activated either by mutations in the consensu...
website       summary

DBCP
The Disulfide Bonding Connectivity Pattern (DBCP) web server tool provides prediction of disulphide bonding connectivity patterns without the prior knowledge of the bonding states of cysteines. Useful in locating disulphide b...
website       summary

dbCRID
A database of Chromosomal Rearrangements In Diseases (dbCRID, http://dbCRID.biolead.org) is a database of human CR events and their associated diseases. For each reported CR event, dbCRID documents the type of the event, the ...
website       summary

dbDEPC
A database of differentially expressed proteins in human cancers (dbDEPC) collects curated cancer proteomics data, provides a resource for information on protein-level expression changes, and explores protein profile differen...
website       summary

dbDNV
The duplicated gene nucleotide variants database (dbDNV) (http://goods.ibms.sinica.edu.tw/DNVs/) promotes accurate variation annotation. Aside from the flat file download, users can explore the gene-related duplications and t...
website       summary

dbEST
Expressed Sequence Tags database; a division of GenBank containing single-pass cDNA sequence reads
website       summary

dbSNP
Repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms; NCBI collaboration with NHGRI.
website       summary

dbSNP-Q
dbSNP-Q is a web application for working with the dbSNP relational database. dbSNP is a source of information on single nucleotide polymorphisms (SNPs) and other genetic variation for many different organisms, including human...
website       summary

DBTSS
DataBase of Transcription Start Sites (DBTSS) is a database which contains precise positional information for transcription start sites (TSSs) of eukaryotic mRNAs. Included are 330 million new tags generated by massively sequ...
website       summary

DCODE.ORG
The dcode.org website provides access to tools for comparative genomic analyses developed by the Comparative Genomics Center at the Lawerence Livermore National Laboratory. Tools include: zPicture, Mulan, eShadow, rVista, CRE...
website       summary

DDBJ
The DNA Data Bank of Japan (DDBJ) provides a nucleotide sequence archive database and accompanying database tools for sequence submission, entry retrieval and annotation analysis. A new archive for quantitative genomics data,...
website       summary

DDI-CPI
DDI-CPI, is a web server that predicts Drug-Drug Interactions through implementing the Chemical-Protein Interactome.
website       summary

DDPC
Dragon Database of Genes associated with Prostate Cancer (DDPC) as an integrated knowledgebase of genes experimentally verified as implicated in PC. DDPC is distinctive from other databases in that (i) it provides pre-compile...
website       summary

DECA
DECA is a species disambiguation system for biological named entities. The system will identify protein entities and disambiguate them according to species, by assigning NCBI Taxonomy organism IDs.
website       summary

deconSTRUCT
deconSTRUCT web server interfaces with a protein database search engine and can be used for the detection of similar protein (sub)structures.
website       summary

DEEP
DEEP (Differential Expression Effector Prediction) is a tool that can identify effectors of specific expression profiles by combining gene expression data with biological expert knowledge about biomolecular interaction networ...
website       summary

deepBase
deepBase contains deep sequencing data from 185 small RNA libraries from diverse tissues and cell lines of seven organisms: human, mouse, chicken, Ciona intestinalis, Drosophila melanogaster, Caenhorhabditis elegans and Arabi...
website       summary

deepTools
deepTools: a flexible platform for exploring deep-sequencing data based on the Galaxy platform.
website       summary

Defining Transcriptional Programs in Vascular Endothelium
This website contains microarray analysis software (Argus and Z-pool), an Endothelial Cell Expression Database, and other resources related to Vascular Endothelium research. See the PubMed abstracts for more information.
website       summary

DeNovoID
DeNovoID is a tool for protein identification using de novo peptide sequence data from mass spectrometry experiments.
website       summary

DePIE
Design Primers for Protein Interaction Experiments (DePIE) is a web-based primer design tool for protein interaction experiments.
website       summary

DEPTH
DEPTH web tool computes depth and solvent-accessible surface area values for the prediction of small molecule ligand binding cavities in proteins.
website       summary

DEQOR
Tool which aids in the design and quality control of small interfering RNAs (siRNAs) for RNA interference (RNAi) and gene silencing. It evaluates the inhibitory potency of potential siRNA sequences as well as identifying gene...
website       summary

DHcL
DHcL provides analysis of the hierarchy of protein domain structures. DHcL detects closed loops and van der Waals locks, and outputs domain decomposition at different levels of protein domain structure hierarchy.
website       summary

DIAL
DIAL (dihedral alignment) is a server that provides access to a dynamic programming algorithm for structural alignment of RNA.
website       summary

DIAL
DIAL (Domain Identification Algorithm) is a web server for the automatic identification of structural domains given the three-dimensional coordinates of a protein.
website       summary

DIALIGN
Multiple alignment program which assembles a global sequence alignment from gap-free local pairwise alignments. This method could be especially useful when comparing large sequences that have only local similarities.
website       summary

DIALIGN-TX
DIALIGN-TX is an update to DIALIGN. It combines the greedy heuristic method of DIALIGN with a traditional progressive method.
website       summary

DIANA-microT
The DIANA-microT web server predicts targets for miRNAs and provides functional information on the predicted miRNA:target gene interaction from various online biological resources. Updates enable the association of miRNAs to ...
website       summary

DiANNA
DiANNA (DiAminoacid Neural Network Application) a tool that predicts cysteine states of a protein. It can predict whether a particular cysteine is reduced, is forming a disulfide bond, or is bound to a metallic ligand.
website       summary

DICHROWEB
A server that supports several different algorithms for the analysis of Circular Dichroism (CD) spectra for the prediction of protein secondary structure. Results also contain a graphical comparison of calculated versus exper...
website       summary

dictyBase update 2011
dictyBase, the model organism database for Dictyostelium, provides well integrated, high quality data and tools for Dictyostelium discoideum and related species. dictyBase houses the complete genome sequence, ESTs, and the en...
website       summary

DILIMOT
Discovery of Linear Motifs (DILIMOT) is a server for finding short (3-8 amino acids) over-represented peptide patterns in a set of proteins.
website       summary

DIMA 3.0
Domain Interaction MAp (DIMA) is a database of predicted and known interactions between protein domains. It integrates 5807 structurally known interactions imported from the iPfam and 3did databases and 46,900 domain interact...
website       summary

DINAMelt
DINAMelt is a tool for predicting hybridization and folding (secondary structure) of DNA and RNA using equilibrium thermodynamic methods.
website       summary

DINIES
DINIES: Drug-target Interaction Network Inference Engine based on Supervised analysis enables the prediction of potential interactions between drug molecules and target proteins, based on drug data and omics-scale protein dat...
website       summary

DIP
The Database of Interacting Proteins (DIP) allows users to search for interacting proteins. Results lists can be searched and/or visualized (statically or dynamically). Users can submit new protein-protein interactions and up...
website       summary

DiRE
A web server for predicting distant (outside of proximal promoter regions) regulatory elements (DiRE) in higher eukaryotic genomces using gene co-expression data, comparative genomics as well as transcription factor binding s...
website       summary

Directory of Open Access Journals
The Directory of Open Access Journals provides a listing of open-access journals and a searchable database of article abstracts from them. It aims to incorporate journals from all subjects and languages.
website       summary

DiscoverySpace
DiscoverySpace is a tool for gene expression analyses and biological discovery.
website       summary

DiseaseConnect
DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections.
website       summary

DisEMBL
A computational tool for prediction of disordered/unstructured regions within a protein sequence.
website       summary

DISULFIND
DISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity given a protein sequence.
website       summary

DMINDA
DMINDA: An integrated web server for DNA motif identification and analyses.
website       summary

DNABINDPROT
DNABINDPROT web tool is designed to predict DNA-binding residues in high frequency modes by the Gaussian network method.
website       summary

DNA Learning Center, Cold Spring Harbor Laboratory
excellent online genetics activities, including BioServers bioinformatics tools designed for teachers and students, and animations explaining techniques such as PCR.
website       summary

DNA Methylation Database
The database contains information about the occurrence of methylated cytosines in the DNA.
website       summary

DNannotator
DNannotator is a tool that performs de novo annotation of SNPs, STSs, and exons. It also allows for the migration of user-defined annotations onto different versions of genomic sequences (<30Kb size limit).
website       summary

DNASU Plasmid Repository
DNASU is a central repository for plasmid clones and collections. DNASU currently stores and distributes over 130,000 plasmids including over 45,000 human and mouse plasmids, full genome collections from numerous organisms, a...
website       summary

DOE Joint Genome Institute Genome Portal
The Joint Genome Institute Genome Portal contains browseable and blastable genome assemblies for several organisms, including Pufferfish, Frog, and Sea squirt.
website       summary

Doelan
Doelan is an tool designed to monitor the quality of DNA microarray production.
website       summary

DOMINE
DOMINE is a collection of known and predicted domain-domain interactions (DDIs) compiled from 15 different sources. The updated DOMINE includes 2285 new domain-domain interactions (DDIs) inferred from experimentally character...
website       summary

d-Omix
A Mixer of Protein Domain Analysis Tools (d-Omix) provides tools to analyze, compare and visualize protein data sets with respect to their combinations of protein domains.
website       summary

Dotlet
Dot plot tool with very helpful learn by example interpretations of sample outputs.
website       summary

DOUTfinder
Domain Outlier Finder (DOUTfinder) is a tool for facilitating protein domain detection among remotely related protein sequences.
website       summary

DRAR-CPI
DRAR-CPI is a web server for the identification of drug repositioning and adverse drug reactions using mining of a chemical-protein interactome.
website       summary

DroID
DroID, the Drosophila Interactions Database, is a comprehensive public resource for Drosophila gene and protein interactions. DroID contains genetic interactions and experimentally detected protein-protein interactions curate...
website       summary

Drosophila DNase I footprint database
Database of transcription factor binding sites created from systematic literature curation and genome annotation of DNase I footprints for Drosophila.
website       summary

DRTF
Database of Rice Transcription Factor (DRTF) is a collection of known and predicted transcription factors from japonica and indica rice genomes.
website       summary

DrugBank
DrugBank is a unique bioinformatics/cheminformatics resource that combines detailed drug (i.e. chemical) data with comprehensive drug target (i.e. protein) information. The database contains >4100 drug entries including >800 ...
website       summary

DrugBank 3.0
DrugBank is a richly annotated database of drug and drug target information. It contains extensive data on the nomenclature, ontology, chemistry, structure, function, action, pharmacology, pharmacokinetics, metabolism and pha...
website       summary

DrugScorePPI
DrugScorePPI web server performs alanine scanning within a given protein-protein complex in silico. Useful for guiding biological experiments and in the development of protein-protein interaction modulators.
website       summary

DRYGin
DRYGIN (Data Repository of Yeast Genetic Interactions)-a web database system that provides a central platform for yeast genetic network analysis and visualization. DRYGIN searches SGA interactions and integrates other data so...
website       summary

DSAP
Deep-Sequencing Small RNA Analysis Pipeline (DSAP) is an automated web service designed to provide analysis of deep sequencing small RNA datasets from the Solexa sequencing platform. Non-coding RNA and miRNA matching are outp...
website       summary

dsCheck
dsCheck takes a nucleotide sequence as input and estimates off-target effects caused by dsRNA (double-stranded RNA) employed in RNAi studies. dsCheck can be used either to verify previously designed dsRNA sequences, or to des...
website       summary

DSHIFT
DSHIFT is a web server for predicting chemical shifts of DNA sequences in random coil form or double helical B-form.
website       summary

DSSPcont
DSSPcont automates protein secondary structure prediction from PDB structures to reflect structural variations due to thermal fluctuations.
website       summary

DUET
DUET is a web server for predicting effects of mutations on protein stability using an integrated computational approach.
website       summary

DynamicProteomics DB
Dynamic Proteomics database contains information on the position and amounts of endogenous proteins in individual living human cells. This is based on the Library of Annotated Reporter Cell-clones (LARC). The Dynamic Proteomi...
website       summary

DynaMine
The DynaMine is a webserver for predicting protein backbone dynamics from protein sequence.
website       summary

DyNAVacS
DyNAVacS is a tool for designing DNA vaccines that includes steps for chosing a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses, and providi...
website       summary

e-RNA
eRNA is a collection of web servers for comparative RNA structure prediction and visualisation.
website       summary

E1DS
E1DS is a web server for enzyme catalytic site prediction. Annotation of enzymes is made using a novel pattern mining algorithm that discovers long sequence motifs.
website       summary

E2G
E2G is a tool that maps a large set of EST and cDNA sequences to a user-supplied genomic sequence. The use of pre-computed indexed data structures increases the efficiency of the sequence comparison process, allowing a large ...
website       summary

E3Miner
E3Miner is a web-based text mining tool that extracts and incorporates comprehensive knowledge about ubiquitin-protein ligases (E3) with their underlying mechanisms. This tool integrates available E3 data from the published l...
website       summary

eBioinformatics
This site provides several bioinformatics software tools packaged together for easy installation on MacOSX computers. The software includes NCBI tools, EMBOSS, ClustalW, Staden, T-Coffee and Primer3.
website       summary

EBI patent sequence database
The EBI Patent Sequence Database is a collection of non-redundant patent sequence databases, which cover the EMBL-Bank nucleotides patent class and the patent protein databases and contain value-added annotations from patent ...
website       summary

EBI Tools
EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOA...
website       summary

EcoCyc
EcoCyc is a comprehensive model organism database for Escherichia coli K-12 MG1655. From the scientific literature, EcoCyc captures the functions of individual E. coli gene products; their regulation at the transcriptional, p...
website       summary

E. coli Genome Project
U. Wisconsin E. coli genome project site maintains and updates the annotated sequence of the E. coli K12 genome. It also has resources and tools such as ASAP for user input on functional annotation and characterization of E. ...
website       summary

ECR Browser
The ECR (Evolutionary Conserved Regions) browser is a web-based tool for visualizing and navigating through whole genome alignments of several vertebrate species. Users can also submit sequences for alignment with one of the ...
website       summary

EDULISS
EDULISS (EDinburgh University Ligand Selection System) database stores structural, physicochemical and pharmacophoric properties of small molecules. For each compound a single 3D conformer is stored along with over 1600 calcu...
website       summary

Effective
Effective is a database of predicted bacterial secreted proteins, implementing two complementary prediction strategies for protein secretion: the identification of eukaryotic-like protein domains and the recognition of signal...
website       summary

eF-seek
eF-seek predicts protein functional sites by searching for similar electrostatic potential and molecular surface shapes against eF-site, a database of electrostatic surfaces for representative ligand binding sites.
website       summary

EGassembler
EGassembler is a pipeline for clustering and assembling sequence fragments from transcript (EST) data or from shotgun sequencing.
website       summary

eggNOG
eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common...
website       summary

e-LEA3D
e-LEA3D web server performs computer aided drug design from molecular fragments. Several design tools are included.
website       summary

Electronic PCR
Find sequence-based markers (STSs) and therefore, map location in a DNA sequence of interest; useful for detecting mis-priming events.
website       summary

ELM
Eukaryotic Linear Motif (ELM) resource is a tool for predicting eukaryotic protein functional sites that report domains, motifs, and sequence patterns based on the input sequence.
website       summary

ElNemo
ElNemo (The Elastic Network Model) is a tool for predicting the possible movements (ie. conformational changes and other structural changes) of macromolecules. This tool allows users to compute, visualize, and analyse low-fre...
website       summary

EMAGE
EMAGE is a freely available online database of in situ gene expression patterns in the developing mouse embryo. Gene expression domains from raw images are extracted and integrated spatially into a set of standard 3D virtual ...
website       summary

EMBL-EBI Framework
The EMBL-EBI framework provides access to a suite of sequence analysis tools. Novel methods of obtaining annotations, integrating domain and functional predictions, and visualizing sequence analysis results are integrated.
website       summary

EMBOSS
Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.
website       summary

EMBRACE Web Service
European Model for Bioinformatics Research and Community Education (EMBRACE) web service consists of EDAM, an ontology for describing life sciences; BioXSD, a schema for exchanging data between services and a centralized regi...
website       summary

EMDataBank.org
EMDataBank.org is a resource for deposition and retrieval of cryoEM maps, models and associated metadata. The resource unifies public access to the two major archives containing EM-based structural data: EM Data Bank (EMDB) a...
website       summary

EMMA
The European Mouse Mutant Archive (EMMA) is an infrastructure for archiving and worldwide provision of mouse mutant strains. It operates in collaboration with the other members of the Federation of International Mouse Resourc...
website       summary

eMolecules
eMolecules is a search engine for chemical structures that allows for substructure searching.
website       summary

ENCODE DCC
The ENCODE project has a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) serves as the central repository for ENCODE data. The DCC contains a collection of high-t...
website       summary

ENDEAVOUR
ENDEAVOUR is a computational approach to prioritize candidate genes for further study. Users input training genes already known to be involved in the process under study and the candidate genes to prioritize. The web server s...
website       summary

ENDscript 2.0
ENDscript is a tool for creating, visualizing, and interpreting multiple sequence alignments overlayed with known structural information.
website       summary

enoLOGOS
enoLOGOS creates sequence logos based on a variety of input, including sequence alignments, probability and alignment matrices and energy measurements.
website       summary

Ensembl
The Ensembl project provides high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene ...
website       summary

Ensembl API
Ensembl is a freely available software system for genomic analysis. The documentation page at Ensembl is the best place to get information on the Ensembl application programming interface (API). In particular, the tutorial do...
website       summary

Ensembl C.elegans Genome Browser
Access the data through the Ensembl user interface (both for visualisation and data mining) to provide cross-species integration throughout Ensembl\'s comparative genomics resources.
website       summary

Ensembl Drosophila Genome Browser
Access to the Fly genome through the Ensembl user interface (both for visualisation and data mining).
website       summary

Ensembl Fugu Genome Browser
Fugu Ensembl is a joint project between The IMCB and the EMBL - EBI to produce and maintain an automatic annotation of the Fugu Genome.
website       summary

Ensembl Genome Browser
Website, MySQL server and perl API access to software system which produces and maintains automatic annotation on eukaryotic genomes.
website       summary

Ensembl Genomes
Ensembl Genomes is a new portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualisation platform. Ensembl Genomes con...
website       summary

Ensembl Human Genome Browser
Website, MySQL server and perl API access to software system which produces and maintains automatic annotation on eukaryotic genomes; uses NCBI assembly.
website       summary

Ensembl Mosquito Genome Browser
This site presents the tenfold whole genome shotgun assembly of the PEST strain of anopheles gambiae, as prepared by The International Anopheles Genome project.
website       summary

Ensembl Mouse Genome Browser
Analysis of finished and draft mouse genomic clone sequences.
website       summary

Ensembl Rat Genome Browser
The Rat Genome project is an international collaboration to sequence the genome of the brown rat (Rattus norvegicus).
website       summary

Ensembl Zebrafish Genome Browser
This ensembl website features the zebrafish whole genome shotgun assembly sequence.
website       summary

EnteriX
EnteriX is a collection of tools for viewing pairwise and multiple alignments for bacterial genome sequences.
website       summary

Entrez
NCBI information retrieval system, including GenBank, MMDB (structures), genomes, population sets, OMIM, taxonomy and PubMed.
website       summary

Entrez Gene
Entrez Gene is NCBI's database for gene-specific information. Entrez Gene maintains records from genomes which have been completely sequenced, which have an active research community to submit gene-specific information, or wh...
website       summary

Entrez Genomes
List of prominent complete genomes with access to BLAST and precomputed conserved domains and protein homologs in complete genome context.
website       summary

Entrez Programming Utilities
The Entrez Programming Utilities provide a method of linking to Entrez and querying the Entrez database outside of the regular web interface. Users can access the utilities via a web address, or via a Simple Object Access Pro...
website       summary

ENZYME - Enzyme nomenclature database
Repository of enzyme nomenclature information; useful selection of cross references to other databases; free for research purposes only.
website       summary

EpiToolKit
A suite of tools for immunological research. EpiToolKit offers a variety of prediction methods that may be run simultaneously for predicting MHC Class I and II ligands, and minor histocompatibility antigens. The influence of ...
website       summary

Eponine
Eponine is a probabilistic method for detecting transcription start sites (TSS) in mammalian genomic sequence, with good specificity and excellent positional accuracy.
website       summary

eProbalign
eProbalign computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities. eProbalign also provides a platform to visualize the alignment, generate images, and manipulate the o...
website       summary

E-RNAi
E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of se...
website       summary

ERPIN
ERPIN (Easy RNA Profile IdentificatioN) takes as input an RNA sequence alignment and secondary structure annotation and will identify a wide variety of known RNA motifs (such as tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hamm...
website       summary

ESEfinder
ESEfinder is a web-based resource for identifing putative ESEs (exonic splicing enhancers), cis-acting motifs responsible for enhancing splicing.
website       summary

eShadow
A tool for phylogenetic shadowing of multiple sequences from closely related species. This analyses of multiple sequence alignments can be used to predict putative functional elements.
website       summary

ESLpred
ESLpred is a tool for predicting subcellular localization of proteins using support vector machines. The predictions are based on dipeptide and amino acid composition, and physico-chemical properties.
website       summary

ESPript 3.0
Easy Sequencing in Postscript (ESPript) is a utility which provides postscript output for aligned sequences with graphical enhancements and structural information.
website       summary

ESTExplorer
ESTExplorer is an automated suite of programs to pre-process, assemble and functionally annotate ESTs at both DNA and protein level.
website       summary

eTBLAST
eTBLAST is a textual similarity search engine. This server can parse and summarize the results of an abstract similarity search to find appropriate journals for publication, authors with expertise in a given field, and docume...
website       summary

Ethical, Legal, and Social Issues - Genome Research
Addresses a variety of ethical issues including genetic testing, gene therapy, privacy and patenting.
website       summary

ET Report Maker
Evolutionary trace (ET) report maker pools information from different sources including databases and on-the-fly multiple sequence analysis to produce a pdf formatted document as output. The emphasis is on prediction of funct...
website       summary

EUGENE'HOM
EUGENE'HOM is a gene prediction software for eukaryotic organisms based on comparative analysis. The data is currently tuned for plant sequences of up to 400kb.
website       summary

euGenes: Genomic Information for Eukaryotic Organisms
Summary of gene and genomic information automatically maintained from primary eukaryotic organism databases: gene symbol, full name, chromosome, genetic and molecular maps, gene products, links to extended gene information.
website       summary

EuPathDB (formerly ApiDB)
EuPathDB (formerly ApiDB) is an integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. The EuPathDB portal offe...
website       summary

Eureka Alert
Daily news updates on science, medicine, health, and technology.
website       summary

The European Bioinformatics Institute (EBI)
The European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interact...
website       summary

European Nucleotide Archive
The European Nucleotide Archive (ENA) is Europe's nucleotide-sequence repository. The ENA consists of three main databases: the Sequence Read Archive (SRA), the Trace Archive and EMBL-Bank. New features include extended EMBL-...
website       summary

EuroPhenome
The EuroPhenome project provides access to raw and annotated mouse phenotyping data generated from primary pipelines such as EMPReSSlim and secondary procedures from specialist centres. Mutants of interest can be identified b...
website       summary

EVA
EValuation of Automatic protein structure prediction; provides a continuous, automated, statistical analysis of structure prediction servers.
website       summary

EVAcon
EVAcon automates the continuous evaluation of inter-residue contact prediction servers. Results can be viewed statically or dynamically generated.
website       summary

EvoCor
EvoCor is a web server for predicting functionally related genes using phylogenetic and expression profiles.
website       summary

ExPASy 2-D PAGE databases and services
References to known 2-D PAGE database servers, as well as to 2-D PAGE related servers and services.
website       summary

ExPASy Molecular Biology Server
ExPASy is the bioinformatics resource portal for access to programs and databases for the analysis of proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc.
website       summary

ExPASy Proteomics tools
Various tools for protein identification and characterization, similarity searches, pattern and profile searches, post-translational modification prediction, and more.
website       summary

Expression Profiler
Expression Profiler is a web based platform for microarray data analysis developed at the EBI. This resource is integrated with the ArrayExpress database, a public repository for microarray data.
website       summary

ExpressYourself
ExpressYourself is a web-based platform to process microarray data. It includes tools for background correction, normalization, data processing and filtering.
website       summary

FABLE
Fast Automated Biomedical Literature Extraction (FABLE) mines the  biomedical literature for information about human genes and proteins. User can find articles mentioning a gene of interest (Article Finder), generate a lis...
website       summary

FACTA+
FACTA+ (Finding Associated Concepts with Text Analysis) is a real-time text-mining system for finding and visualizing indirect associations between biomedical concepts from MEDLINE abstracts. The system can be used as a text ...
website       summary

FAF-Drugs
Free ADME/tox Filtering (FAF-Drugs) allows users to process their own compound collections via simple absorption, distribution, metabolism, excretion and toxicity (ADME/tox) filtering rules to aid in the drug discovery proces...
website       summary

FALC-Loop
The FALC-Loop web server allows for protein loop modeling by employing the fragment assembly and analytical loop closure (FALC) loop modeling method.
website       summary

FANTOM
The Functional Annotation Of the Mammalian Genome (FANTOM) is a database for the transcriptional network that regulates macrophage differentiation. Data comes from cap analysis of gene expression (CAGE), sequencing mRNA 5'-en...
website       summary

FANTOM - Functional Annotation of Mouse
Functional annotations for RIKEN full-length cDNA clones.
website       summary

FASTA Programs
Sequence retrieval and comparison tools.
website       summary

FastContact
FastContact is a free energy scoring tool for protein-protein complex structures.
website       summary

fastSCOP
fastSCOP identifies structural domains and determines evolutionary superfamilies of a query protein structure using 3D-BLAST to scan SCOP and MAMMOTH to create a structural alignment for refining domain boundaries.
website       summary

FastSNP
Function Analysis and Selection Tool for Single Nucleotide Polymorphisms (FastSNP) allows users to identify and prioritize SNPs that are likely to have functional effects.
website       summary

FATCAT
FATCAT provides the means to compare two PDB-format protein structures, or to search for structures similar to a given PDB structure. The user can supply a PDB ID or upload a structure file. The FATCAT web server employs the ...
website       summary

FatiGOplus
FatiGOplus is a tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, FatiGOplus finds differential distributions of biologica...
website       summary

FeatureExtract
The FeatureExtract server extracts sequence and feature annotations, such as intron/exon structure, from GenBank entries and other GenBank format files.
website       summary

FeatureMap3D
FeatureMap3D is a tool to map protein features and sequence conservation onto homologous structures in PDB.
website       summary

FeatureScan
FeatureScan searches for sequence similarity by comparing physico-chemical properties of DNA such as charge, melting enthalpy, conformational parameters, etc.
website       summary

FFAS
The Fold & Function Assignment System (FFAS) takes an amino-acid sequence as input and generates a profile which is compared to several sets of sequence profiles including PDB, SCOP, and PFAM. Public metagenomic sequence data...
website       summary

FF - Fragment Finder
FF (Fragment Finder) takes a PDB ID, a structure coordinate file or a list of phi and psi angles as input and searches for matches to a specified structural fragment. Users can tailor the search based on sequence similarity a...
website       summary

FFPred
Using a machine learning approach, FFPred server predicts protein function using protein features scanned against a library of over 300 Gene Ontology annotation terms. FFPred has the capacity to annotate distant homologues an...
website       summary

FGDB
The MIPS Fusarium graminearum Genome Database (FGDB) is a comprehensive genome database for Fusarium graminearum. The current version of FGDB v3.1 provides information on the full manually revised gene set based on the Broad ...
website       summary

FGF
FGF (Fishing Gene Family) is a resource for finding gene families given a set of protein sequences by investigating phylogenetic trees, duplication fate, and selective pressure (ka/ks calculations).
website       summary

FiberDock
FiberDock is a docking refinement web server that accounts for backbone and side-chain flexibility. Potential docking structures are scored according to an energy function.
website       summary

FINDbase
Frequency of INherited Disorders database (FIND base) records frequencies of causative genetic variations worldwide. Database records include the population and ethnic group or geographical region, the disorder name and the r...
website       summary

FireDock
The FireDock web server performs high-throughput flexible refinement and scoring of protein-protein docking solutions. Side chain conformations and rigid body orientations are optimized, and outputs viewed in three-dimensiona...
website       summary

firestar
Firestar predicts functionally important residues, such as catalytic and ligand binding sites, using structural templates and alignment reliability. Prediction coverage has increased with the extension of the FireDB and ligan...
website       summary

FirstEF
First Exon Finder (FirstEF) is a 5\' terminal exon and promoter prediction program. It consists of different discriminant functions structured as a decision tree.
website       summary

FISH
Family Identification with Structure Anchored HMMs (FISH) is a server for the identification of remote sequence homologues on the basis of protein domains.
website       summary

FluGenome
FluGenome is a tool for determining lineages and genotypes of influenza A viruses.
website       summary

FlyBase
FlyBase is a database of genetic and molecular data for Drosophila. FlyBase includes data on all species from the family Drosophilidae; the primary species represented is Drosophila melanogaster.
website       summary

FlyFactorSurvey
FlyFactorSurvey is a database of DNA binding specificities for Drosophila transcription factors (TFs) determined using the bacterial one-hybrid system. The database provides to recognition motifs and position weight matrices ...
website       summary

FlyTF
FlyTF is a database of computationally predicted and/or experimentally verified site-specific transcription factors (TFs) in the fruit fly Drosophila melanogaster. This database contains information on the manual curation of ...
website       summary

FMM
From Metabolite to Metabolite (FMM) is a web server for metabolic pathway reconstruction from one metabolite to another metabolite in a different species based on the KEGG pathway and other integrated databases.
website       summary

FOLDALIGN
FOLDALIGN is an algorithm for local simultaneous folding and aligning two or more RNA sequences.
website       summary

FoldMiner and LOCK 2
FoldMiner aligns a user-supplied or identified query structure to a database of single domain targets to discover structural neighbours and characteristic motifs. Query structures can also be aligned to one or more user-speci...
website       summary

FOLDOC - Computing Dictionary
FOLDOC (Free Online Dictionary of Computing) is a good place to look up meanings of computer jargon.
website       summary

FOLD-RATE
FOLD-RATE predicts the folding rates of proteins from their amino acid sequences.
website       summary

FoldX
FOLD-X is a program for calculating the folding energies of proteins and for calculating the effect of a point mutation on the stability of a protein.
website       summary

Footer
Footer is a tool for identifying highly-probable binding sites of known transcription factors using phylogenetic footprinting principles to analyse two homologous DNA sequences.
website       summary

FoXS
Fast X-ray Scattering (FoXS) is a web server for computing the small angle x-ray scattering (SAXS) structure profile of a molecule in solution and for comparing the computed profile to the experimental profile.
website       summary

Fpocket
Fpocket web server detects small molecule pockets by relying on the geometric alpha sphere theory. It also tracks pockets during molecular dynamics so to provide insight on pocket dynamics (mdpocket) and transposes mdpocket t...
website       summary

fPOP
fPOP (footprinting Pockets Of Proteins) is a relational database of the protein functional surfaces identified by analyzing the shapes of binding sites in approximately 42,700 structures, including both holo and apo forms. To...
website       summary

FragmentStore
FragmentStore, a resource for the comparison of fragments found in metabolites, drugs or toxic compounds. Starting from 13,000 metabolites, 16,000 drugs and 2200 toxic compounds we generated 35,000 different building blocks (...
website       summary

FrameD
FrameD is a program that predicts coding regions in prokaryotic and eukaryotic sequences that may contain frameshifts.
website       summary

Freiburg RNA Tools
The Freiburg RNA Tools web server contains tools for the advanced analysis of RNA. The tools IntaRNA, ExpaRNA and LocARNA support the prediction of RNA-RNA interaction, exact RNA matching and alignment of RNA, respectively.
website       summary

Frog
Frog (Free Online Drug Conformation) is a service aimed at generating 3D conformations for drug-like compounds starting from their 1D or 2D descriptions (smiles or sdf).
website       summary

Frog2
Frog2 (Free Online Drug Conformation 2) is a service aimed at generating 3D conformations for small molecules starting from their 1D, 2D or 3D descriptions (smiles, sdf or mol2 input formats). Frog2 improves upon Frog1 by emb...
website       summary

Full-parasites
Full-Parasites is a transcriptome database of apicomplexa parasites, which include Plasmodium and Toxoplasma species. It contains EST sequences, full length cDNAs, transcription start sites and RNA-seq data sets. Various type...
website       summary

FunShift
FunShift is a database that stores Pfam subfamily classification for protein domain families and analyses them for functional changes using evolutionary substitution rates and conservation shifts.
website       summary

FunSimMat
FunSimMat is a functional similarity database and web service for ranking genes/proteins by function. It provides different semantic similarity measures for Gene Ontology terms and offers functional similarity values for prot...
website       summary

G2D
G2D (Candidate Genes to Inherited Diseases) scans a human genomic region for genes related to an inherited disease. The G2D server also presents precomputed candidate genes for more than 600 genetically inherited diseases tha...
website       summary

Galaxy
Galaxy is an open, web-based platform for performing accessible, reproducible, and transparent biomedical research. Complete computational analyses can be built, saved, rerun, modified and shared. Galaxy is available as a fre...
website       summary

GalaxySite
GalaxySite is a web server for ligand-binding site prediction by using molecular docking.
website       summary

GC-Profile
GC-Profile is a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences.
website       summary

GCUA: Graphical Codon Usage Analyser
Graphical representation of codon bias
website       summary

GCView
GCView facilitates the analysis of the genomic context of a query protein. It uses protein homology to assign corresponding genomic context.
website       summary

GDAP
The Genomic Disulfide Analysis Program (GDAP) predicts disulfide bonds for a user-supplied protein sequence. GDAP also provides access to pre-computed predictions of disulfide bonds for over 100 microbial genomes.
website       summary

GeConT 2
The Gene Context Tool (GeConT) is a visualization tool for viewing the genomic context of a gene or group of genes, and their orthologous relationships, within any of the fully sequenced bacterial genomes. Sequence retrieval ...
website       summary

GELBANK
GELBANK is a database of 2D gel images of proteomes for species with completed genomes. The user can search by sequence description or fragment, or by gel characteristics. Links are made between the sequence and gel when avai...
website       summary

GelScape and GelBank
GelScape is a platform-independent 1D and 2D gel analysis system that is freely available. Features include the ability to mark spots, to measure spot intensities and to archive gel images and annotations to the public databa...
website       summary

Gemina
The Gemina system provides an integrated investigative and geospatial surveillance system connecting pathogens, pathogen products and disease anchored on the taxonomic ID of the pathogen and host to identify the breadth of ho...
website       summary

GeMprospector
GeMprospector is designed to find cross-species genetic marker candidates in legumes and grasses. GeMprospector automates PCR primer design based on multiple sequence alignments of submitted ESTs and their homologues in seque...
website       summary

GEMS
GEMS (Gene Expression Mining Server) is a tool for biclustering microarray data. It is available as a web tool and as a standalone command-line program.
website       summary

GenBank
GenBank is a comprehensive database that contains publicly available nucleotide sequences for more than 300,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories ...
website       summary

GenDecoder
GenDecoder is a prediction server for animal mitochondrial genetic codes. It provides information about codon-usage, amino acid composition, GC content and a final genetic code prediction for a mitochondrial genome sequence.
website       summary

Gendoo
Gene Disease Features Ontology-based Overview System (Gendoo) is a web tool for visualizing disease feature profiles generated from the assignment of MeSH vocabulary for associated drugs, biological phenomena and anatomy to O...
website       summary

Gene2Oligo
Tool which divides both strands of an input DNA sequence into a set of contiguous oligonucleotides. These oligos are designed with complimentary regions so that the complete set can be combined to synthesize the input DNA seq...
website       summary

Gene3D
Gene3D provides accurate structural domain family assignments for over 1100 genomes and nearly 10,000,000 proteins. A hidden Markov model library, constructed from the manually curated CATH structural domain hierarchy, is use...
website       summary

Gene3D
The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to...
website       summary

GeneCards
Database of human genes, their products, and involvement in diseases; free for non-commercial use, but users should also read the Terms of Use for this site.
website       summary

GeneCAT
The Gene Co-expression Analysis Tool-box (GeneCAT) is a suite of microarray co-expression analysis tools for plant biology. The platform includes both standard co-expression tools such as gene clustering and expression profil...
website       summary

GeneCodis3
Originally designed in 2007 for modular enrichment analysis, GeneCodis assists in functional analysis of gene lists, integrating information from different sources. GeneCodis also finds regulatory patterns, and singular and m...
website       summary

GeneDB
The GeneDB projects primary goal is to develop and maintain curated database resources for three organisms: Schizosaccharomyces pombe, the kinetoplastid protozoa Leishmania major, and Trypanosoma brucei.
website       summary

GeneDoc
Multiple sequence alignment editor, analyser and shading utility for Windows.
website       summary

GeneExpress2.1
Integrated system for data analysis with information about expression and gene networks, also contains transcriptional regulatory regions database (TRRD).
website       summary

Gene Expression Barcode
Gene Expression Barcode is a database that provides reliable absolute measures of expression for most annotated genes for human and mouse tissue types, including diseased tissue. This is made possible by an algorithm that lev...
website       summary

Gene Expression Data Analyzer
The Gene Expression Data Analyzer (GEDA) is a tool for discovering differential gene expression in a subset of patients. It is tailored to cancer-related microarray studies and offers extensive options for visualization, clas...
website       summary

Gene Expression Database (GXD)
The Gene Expression Database (GXD) is a community resource of mouse developmental expression information. GXD integrates different types of expression data at the transcript and protein level and captures expression informati...
website       summary

Genefisher
Interactive primer design tool for standard or degenerate primers; will accept unaligned sequences.
website       summary

GeneFizz
GeneFizz is a tool for identifying genes using by using the physical characteristics of helix-to-coil transitions in DNA.
website       summary

GeneGenie
GeneGenie is an optimised oligomer design web server for doing directed evolution.
website       summary

GeneHub-GEPIS
GeneHub-GEPIS is a tool for inferring human and mouse gene expression patterns based on normalized EST abundance in various normal and cancerous tissues.
website       summary

GeneMANIA
GeneMANIA is web interface for generating hypotheses about gene function, analyzing gene lists and prioritizing genes for functional assays. Users input a query list for extension and weighting with functionally similar genes...
website       summary

GeneMark
The GeneMark family of programs employ Markov models and are specifically tuned for gene prediction for sequences from prokaryotes, viral genomes and eukaryotes.
website       summary

genenames.org
genenames.org displays all approved nomenclature within Symbol Reports that contain data curated by HUGO Gene Nomenclature Committee (HGNC) editors and links to related genomic, phenotypic and proteomic information. New featu...
website       summary

GenePath2
GenePath is a tool for automated construction of genetic networks and proposal of genetic experiments from mutant data.
website       summary

GenePattern 2.0
GenePattern combines a powerful scientific workflow platform with more than 100 genomic analysis tools. An intuitive web interface makes it easy to use.
website       summary

GenePublisher
GenePublisher performs automatic normalization, statistical analysis, and visualization of DNA microarray data.
website       summary

Gene Regulation
Access to databases, programs and papers related to gene regulation.
website       summary

GeneSeeker
GeneSeeker allows you to generate a list of candidate genes related to a human genetic disorder by searching against localization and expression databases.
website       summary

GeneSeqer
GeneSeqer is a method to identify exon/intron structure by splice site prediction and spliced alignment in plant genomes.
website       summary

GeneSet2miRNA
GeneSet2miRNA is a web based tool for identification of miRNA regulatory activity within an input gene list. A list of miRNA regulatory models is output.
website       summary

Gene Set Builder
Gene Set Builder is a database-driven, web-based tool designed to help researchers compile, store, export, and share sets of genes. This application supports the 17 eukaryotic genomes found in version 32 of the Ensembl databa...
website       summary

GeneSigDB
GeneSigDB is a manually curated database of gene expression signatures. GeneSigDB focuses on cancer, development, and stem cell gene signatures and was constructed from thousands of publications from which we manually transcr...
website       summary

GeneSplicer
A fast, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been trained and tested successfully on Plasmodium falciparum (malaria), Arabidopsis thaliana, human, Drosophila, and...
website       summary

GeneTests
GeneTests is a medical genetics information resource developed for physicians, other healthcare providers, and researchers, available at no cost to all interested persons
website       summary

Genethics.ca - The Genetics & Ethics page
The goal of this site is to serve as a clearing house for information on the social, ethical and policy issues associated with genetic and genomic knowledge and technology.
website       summary

GeneTrail
GeneTrail analyzes gene sets for statistically significant accumulations of genes belonging to functional categories. Two common statistical approaches are implemented including: Over-Representation Analysis (ORA) for compari...
website       summary

Gene Wiki
The Gene Wiki goal is to build a gene-specific review article for every gene in the human genome, where each article is collaboratively written, continuously updated and community reviewed. Gene Wiki articles are freely acces...
website       summary

GenMAPP
GenMAPP (Gene MicroArray Pathway Profiler) is a microarray expression data visualization tool, allowing data to be viewed on maps representing gene groupings and biological pathways.
website       summary

GeNMR
Generate NMR structures (GeNMR) is a web server for generating 3D protein structures using input sequence data, NOE-based distance restraints or NMR chemical shifts. Output is a set of PDB coordinates for the input protein.
website       summary

Geno2pheno
Geno2pheno takes as input an HIV-1 pol-gene DNA sequence and estimates phenotypic drug resistance to 17 antiretroviral drugs.
website       summary

GenoCAD
GenoCAD is a web-based application for designing protein expression vectors, artificial gene networks and other genetic constructs composed of multiple functional blocks. Users can download the designed sequence for synthesis...
website       summary

Genome British Columbia's Learning Centre
Aimed to keep the general public informed about the science, technology and issues connected with genomics and proteomics.
website       summary

Genome Canada
The primary funding resource relating to genomics and proteomics in Canada.
website       summary

Genome Centres and Databases
Genome centers and databases listed by organism.
website       summary

Genome Database for Rosaceae
Genome Database for Rosaceae (GDR) contains all publically available Rosaceae sequences including annotated peach, strawberry and almond EST sequences and the genetically anchored peach physical map.
website       summary

Genome Hub
Lists of genome-related sites maintained by the NHGRI on behalf of the International Human Genome Sequencing Consortium.
website       summary

GenomeNet
Network of database and computational resources including KEGG (pathways, interactions, etc.) and DBGET/LinkDB (an integrated database retrieval system). It also hosts several web-based tools for sequence analysis (ie. Blast,...
website       summary

Genome News Network
Bi-weekly online news magazine, covering genomics, proteomics, and related news in biomedical, microbial, and agricultural research; publication of The Institute for Genomic Research (TIGR).
website       summary

GenomeRNAi
The GenomeRNAi database contains phenotypes from published cell-based RNA interference (RNAi) screens in Drosophila and Homo sapiens. The database connects observed phenotypes with annotations of targeted genes and informatio...
website       summary

GenomeScan
Incorporates protein similarity information when predicting genes; based in part on GENSCAN.
website       summary

Genome Surveyor
Genome Surveyor is a tool for discovery and analysis of cis-regulatory elements and transcription factors in Drosphila built on the GBrowse genome browser.
website       summary

GenomeTraFaC
GenomeTraFaC is a comparative genomics based resource for initial characterization of gene models and the identification of putative cis-regulatory regions of RefSeq gene orthologs.
website       summary

Genome Web
News reports on the business and technology of genomics, updated continuously throughout the business day.
website       summary

Genotyping - NCBI
The Genotyping tool at the NCBI identifies the genotype (or subtype) of viral sequences by using a sliding window approach to BLAST analysis against reference sequences for different viral subtypes. Results are shown as a gra...
website       summary

GENSCAN
Identification of complete gene structures in genomic DNA.
website       summary

GEPAS
The Gene Expression Pattern Analysis Suite (GEPAS) is a collection of tools for the analysis of microarray data. GEPAS includes tools for data pre-processing, clustering, differential gene expression, predictors, array CGH an...
website       summary

GeSBAP
Gene Set based Analysis of Polymorphisms (GeSBAP) implements the gene set analysis to the evaluation of genome wide association studies. Gene set analysis is based on testing the association of modules of functionally related...
website       summary

GFINDer
Genome Functional INtegrated Discoverer (GFINDer) takes a list of gene/clone IDs with classification information as input, and allows the user to characterize the different gene classes in the list using annotations of variou...
website       summary

Gibbs Motif Sampler
Gibbs Motif Sampler allows you to identify motifs, conserved regions, in DNA or protein sequences. This tool can be applied for the detection of transcription factor binding sites (TFBS).
website       summary

GIS
GIS (Gangsta+ internet services) allows users to analyze protein structure families according to the SCOP classification scheme. Users can upload their own protein structures for pair-wise protein structure comparison, struct...
website       summary

GLAMM
GLAMM is a web server for visualizing metabolic networks, reconstructing metabolic networks from annotated genome data, visualizing experimental data in the context of metabolic data and investigating the construction of nove...
website       summary

G-language GAE
G-language Genome Analysis Environment (G-language GAE) is a compendium of more than 100 programs that focus on bacterial genome analysis. Included are programs for identification of binding sites, analysis of codons and pred...
website       summary

Glimmer
Gene Locator and Interpolated Markov Modeler; this prokaryote-gene finding tool is the primary microbial gene finder used at TIGR; free (including source code) with registration for non-commercial use.
website       summary

The Global Proteome Machine
The Global Proteome Machine (GPM) project facilitates the analysis of proteomes for researchers using tandem mass spectrometry. The aims of the project include providing a common validation and testing platform for results, m...
website       summary

GlobPlot
GlobPlot has the ability to plot the tendency towards globularity for a given protein sequence. Can also perform SMART/Pfam domain prediction.
website       summary

Glossary of Genetic Terms, NHGRI
Includes audio explanations of terms by researchers in the relevant field of study; Francis Collins explains shotgun sequencing.
website       summary

GLUE, GLUE-IT, PEDEL, PEDEL-AA and DRIVeR
GLUE, PEDEL, and DRIVeR are tools for estimating completeness and diversity in randomized protein-encoding libraries; useful for guiding library design and for analyzing results. GLUE Including Translation (GLUE-IT) finds the...
website       summary

GlycomeDB
GlycomeDB integrates the structural and taxonomic data of all major public carbohydrate databases, as well as carbohydrates contained in the Protein Data Bank. The database is a unified resource for carbohydrate structures. G...
website       summary

GlycoViewer
The GlycoViewer is a web-based tool that can visualize, summarize and compare sets of gylcan structures.
website       summary

GlyNest and CASPER
GlyNest and CASPER are two independent services, available through this common interface, for predicting NMR spectra given a glycan chemical structure.
website       summary

Glyprot
Glyprot is a tool for predicting and modelling all potential N-glycosylation sites in a given 3D structure.
website       summary

Génie
Genie evaluates the literature attached to all genes in a genome and to their orthologs for a selected topic. Hundreds of species and millions of genes are supported. Running times range from a few seconds to a minute in most...
website       summary

GNN\'s Genomics Glossary
A glossary of Genomics-related terms from the Genome News Network.
website       summary

GO
The Gene Ontology (GO) Consortium (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. Several new relationship types have been in...
website       summary

GOblet
GOblet allows the user to BLAST one or more protein or nucleotide sequences against databases that have sequences mapped to Gene Ontology (GO) terms. Results can be viewed for individual sequences, or as survey statistics for...
website       summary

Godzilla
The Berkeley Genome Pipeline a.k.a. Godzilla, provides precomputed VISTA plots of sequence conservation between pairs of human, mouse or rat genomes.
website       summary

GOEAST
Gene Ontology Enrichment Analysis (GOEAST) is a toolkit for the identification of over-represented GO terms in a given gene set. Distinguishing features include: capacity to analyze data from various sources and from multiple...
website       summary

GoGene
GoGene performs high-throughput text mining to complement annotation of genes. GoGene supports search for genes in PubMed, EntrezGene and BLAST.
website       summary

GOLD
The Genomes On Line Database (GOLD) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed...
website       summary

GoPubMed
GoPubMed is a tool that allows users to explore the results of PubMed queries in the context of Gene Ontology (GO) terms.
website       summary

GoSurfer
GoSurfer is a tool for visualizing and comparing gene sets by mapping them onto Gene Ontology (GO) information in the form of a hierarchical tree. It is useful for investigating the results of microarray analyses or genome-wi...
website       summary

GPCRDB
The GPCRDB is a Molecular Class-Specific Information System (MCSIS) that collects, combines, validates and disseminates large amounts of heterogeneous data on G protein-coupled receptors (GPCRs). The GPCRDB contains experimen...
website       summary

GPCRpred
GPCRpred is a tool that uses a support vector machine based method to make GPCR family and subfamily predictions for a user-supplied query sequence.
website       summary

GPCRsclass
GPCRsclass is a tool for predicting amine-binding receptors based on a protein sequence provided by the user.
website       summary

g:Profiler
g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conver...
website       summary

GPS
Using datasets of known phosphorylation sites, the Group based Phosphorylation Scoring method (GPS) allows the prediction of kinase specific phosphorylation sites from primary protein sequences.
website       summary

GPS-SUMO
GPS-SUMO (small ubiquitin-like modifiers) is a tool for the prediction of sumoylation sites and SUMO-interaction motifs in proteins.
website       summary

GPSDB
Gene and Protein Synonym DataBase (GPSDB) is a collection of gene and protein names, organized by species that can be used to search for a given gene/protein name, retrieve all synonyms for this entity, and query Medline with...
website       summary

GPU.proton.DOCK
Genuine Protein Ultrafast proton equilibria consistent DOCKing (GPU.proton.DOCK) is a tool for in silico prediction of protein-protein interactions via ultrafast docking that considers electrostatic interactions and proton eq...
website       summary

Gramene database in 2010
The Gramene database has become a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice. Gramene has an Ensembl genome browser an...
website       summary

GRAMM-X
GRAMM-X is a protein docking server.
website       summary

GRAPE: GRaphical Abstracted Protein Explorer
GRaphical Abstracted Protein Explorer (GRAPE) is a web server that allows users to explore abstracted representations of proteins. Large scale structural features are preserved while other surfaces are effectively reduced.
website       summary

GraphWeb
GraphWeb is a web server for biological network analysis and module design using a graphical interface.
website       summary

GreenPhylDB v2.0
GreenPhylDB is a database designed for comparative and functional genomics based on complete genomes. It contains full genomes of members of the plantae kingdom, ranging from algae to angiosperms, automatically clustered into...
website       summary

The GRID - General Repository for Interaction Datasets
Database of genetic and physical interactions; contains interaction data from several genome/proteome wide-studies, the MIPS database, and BIND; provides a powerful visualization system for looking at interactions graphically...
website       summary

GRIFFIN
GRIFFIN (G-protein-Receptor Interacting Feature Finding INstrument) uses a support vector machine and hidden markov model to predict G-protein coupled receptors (GPCRs) and G-protein coupling selectivity.
website       summary

GSA-SNP
GSA-SNP web server performs gene set analysis (GSA) on genome-wide association data, using 3 different GSA methods.
website       summary

G-SESAME
G-SESAME is a suite of online tools for measuring the semantic similarities of Gene Ontology (GO) terms and the functional similarities of gene products, as well as data mining the GO database.
website       summary

GUIDANCE
The GUIDANCE web server assesses alignment confidence scores for the identification of unreliable alignment regions. Users input a set of unaligned sequences; output is a graphic visualization of the alignment with confidence...
website       summary

GVS
Genome Variation Server (GVS) is a database that provides access to human genotype data found in dbSNP, and tools for the analysis of genotype data.
website       summary

GWIDD
Genome-wide docking database (GWIDD) is an integrated resource for structural studies of protein-protein interactions on the genome scale, which combines the available experimental data with models obtained by docking techniq...
website       summary

GXA
The Gene Expression Atlas is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biological/experiment...
website       summary

Gypsy Database (GyDB)
Gypsy Database of Mobile Genetic Elements (GyDB)is a database of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). GyDB now includes long terminal repeats (LTR) ret...
website       summary

H++
H++ is an automated tool for computing pK values of ionizable groups in macromolecules and adding missing hydrogen atoms according to the specified pH of the environment. Given a (PDB) structure file on input, H++ outputs the...
website       summary

HapEdit
HapEdit is a tool for assessing the accuracy of assembled haplotypes. Editting functions such as breaking erroneous haplotype segments into smaller segments or concatenating haplotype segments are also possible.
website       summary

Harmony
Harmony is a server to assess the compatibility of an amino acid sequence with a proposed three-dimensional structure.
website       summary

H-DBAS
H-DBAS is a specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs. RNA-Seq tag information is correlated to the AS exons and splice junctions. A total of 148,376,598 RNA-Seq tags h...
website       summary

HexServer
A FFT-based protein docking server powered by graphics processors, HexServer rapidly produces a ranked list of docking predictions for input PDB protein structures.
website       summary

HGNC: HUGO Gene Nomenclature Committee
The HGNC approves a unique gene name and symbol for each known human gene. The HGNC Database is searchable and contains all approved symbols. For each symbol, if known, the database associates gene location, aliases, previous...
website       summary

HGVbase
Human Genome Variation database - curated; attempt to summarize all known sequence variations in the human genome, to facilitate research into how genotypes affect common diseases, drug responses, and other complex phenotypes...
website       summary

HHMD
Human Histone Modification Database (HHMD) focuses on the storage and integration of histone modification datasets that were obtained from laboratory experiments. HHMD incorporates 43 location-specific histone modifications i...
website       summary

HHomp
HHomp is a web server for prediction and classification of outer membrane proteins (OMPs). Beginning with sequence similarity of a protein to known OMPs, HHomp builds a hidden markov model (HMM) and compares the input sequenc...
website       summary

HHpred
Based on the comparison of profile HMMs, HHpred takes a protein sequence or multiple sequence alignment as input and searches for remote homologues in an assortment of databases such as PDB, SMART and Pfam. The user can selec...
website       summary

HHrep
HHrep is a tool for the de novo identification of repeats in protein sequences based on the pairwise comparison of profile hidden Markov models (HMMs).
website       summary

HHsenser
HHsenser is a tool for sensitive iterative sequence searching based on HMM-HMM comparison. Starting from a single sequence or an alignment, HHSenser is able to build alignments with as many near or remote homologs as possible...
website       summary

H-InvDB
The H-Invitational Database (H-InvDB) is a comprehensive annotation resource of human genes and transcripts. The latest release of H-InvDB (release 6.2) provides the annotation for 219,765 human transcripts in 43,159 human ge...
website       summary

HIT
A comprehensive and fully curated database for Herb Ingredients' Targets (HIT). Those herbal ingredients with protein target information were carefully curated. The molecular target information involves those proteins being d...
website       summary

HitPredict
HitPredict is a database with quality assessed PPIs in nine species. HitPredict assigns a confidence level to interactions based on a reliability score that is computed using evidence from sequence, structure and functional a...
website       summary

HLungDB
The human lung cancer database (HLungDB) is a database with the integration of the lung cancer-related genes, proteins and miRNAs together with the corresponding clinical information. Currently, we have collected 2585 genes a...
website       summary

HMDB
The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. The database supports extensive text, sequence, chemical...
website       summary

HMMER
HMMER is an implementation of profile HMM methods for sensitive database searches using multiple sequence alignments as queries.
website       summary

HMMER Web Server
HMMER Web Server is a tool for interactive sequence similarity searching. Methods are available for single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence databases, and for sear...
website       summary

HMMgene
Prediction of vertebrate and C. elegans genes.
website       summary

HMS-ICS
The Hyperlink Management System (HMS) automatically updates and maintains hyperlinks among major databases using various data IDs (e.g. HUGO Gene Symbols, IDs from PDB, UniProt). The ID Converter System (ICS) supports the con...
website       summary

HomozygosityMapper
A web base approach to homozygosity mapping. Users upload SNP genotype or sequencing files for analysis and detection of long homozygous stretches between affected individuals. Human, rodent and other mammals are mappable.
website       summary

HorA
HorA (Homology or Analogy) is a web server that identifies likely homologs for a given query protein structure. HorA combines sequence information with structure information from spatial similarity measures.
website       summary

HotPoint
HotPoint web server predicts hot spots in protein interfaces using an empirical model. Input is a protein complex and two chain identifiers that form an interface; output includes an interactive 3D visualization of the hot sp...
website       summary

HotSpot Wizard
HotSpot Wizard is a web server for automatic identification of hot spots for engineering enzymes with substrate specificity, activity or enantioselectivity and for annotation of protein structures. Hot spots for mutagenesis a...
website       summary

How to Use the Human Draft Sequence
Introduction to how the draft sequence of the human genome can be used by biologists, includes examples of the types of questions that can be answered with the data.
website       summary

HRTBLDb
The Hormone Receptor Target Binding Loci, HRTBLDb database contains hormone receptor binding regions (binding loci) from in vivo ChIP-based high-throughput experiments as well as in silico, computationally predicted, binding ...
website       summary

Hubba
Hub Objects Analyzer or Hubba is a web-based service for characterizing nodes of importance within a protein interactome data set.
website       summary

HubMed
HubMed uses information from PubMed's database, provided by the NCBI through the EUtils web service, to produce a search interface focused on browsing, organising and gathering information from the biomedical literature.
website       summary

Human Ageing Genomic Resources
The Human Ageing Genomic Resources (HAGR) website provides tools and curated databases relevant to the genetics of human ageing. GenAge is a database of genes related to human ageing, and AnAge is a multi-species database fac...
website       summary

Human Gene Mutation Database
The Human Gene Mutation Database comprises various types of mutation within the coding regions of human nuclear genes causing inherited disease.
website       summary

Human Genome Variation Nomenclature
The Human Genome Society has established a committee to suggest standards for the description of sequence variants in DNA, RNA, and protein sequences. The standards are linked here.
website       summary

HUMan MOLecular GENetics Portal Site
The HUMan MOLecular GENetics Portal Site (HUM-MOLGEN) is a source of various types of information related to human molecular genetics, including: news, lists of and links to biomedical companies and journals, job and event li...
website       summary

Human Protein Reference Database
The Human Protein Reference Database (HPRD) is a centralized resource for information about human proteins, their interactions with other human proteins, and protein-disease relationships. The information contained in HPRD is...
website       summary

HumGen
Access to a comprehensive international database on the legal, social and ethical aspects of human genetics.
website       summary

HUPO Proteomics Standards Initiative
HUPO Proteomics Standards Initiative (PSI) provides data representation standards to facilitate the exchange, comparison and validation of proteomics data.
website       summary

Hymenoptera Genome Database
The Hymenoptera Genome Database (HGD) is a comprehensive model organism database for insect species of the order Hymenoptera. HGD contains data from 9 different species across 200 million years in the phylogeny of Hymenoptera...
website       summary

I2I-SiteEngine
Interface-to-Interface (I2I)-SiteEngine compares pairs of interacting protein binding sites by recognizing similarity of physico-chemical properties and shapes in the protein-protein interfaces.
website       summary

IBIS
IBIS is the NCBI Inferred Biomolecular Interaction Server. This server organizes, analyzes and predicts interaction partners and locations of binding sites in proteins. IBIS provides annotations for different types of binding...
website       summary

IBM Bioinformatics and Pattern Discovery Group
Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also e...
website       summary

IBWS: IST Bioinformatics Web Services
The Bioinformatics group at the National Cancer Research Institute (IST) of Genoa compiled a suite of free web services IBWS.
website       summary

IC50-to-Ki
A web-based tool for estimating Ki values from experimentally determined IC50 values for inhibitors of enzymes and of binding reactions between macromolecules and ligands.
website       summary

Iccare
The Iccare (Interspecific Comparative Clustering and Annotation foR Est) web server compares all available EST and mRNA sequences for a query organism against the set of transcripts for a reference organism. The results are p...
website       summary

iCE - internet Contig Explorer
Viewer for physical map data (for mouse, rat, cow, Cryptococcus); developed at the Genome Sciences Centre, Vancouver.
website       summary

ICGEBnet Protein Tools
ICGEBnet Protein Tools is a resource for analysis of 3D protein structures including domain predictors, a protein fold similiarity server (PRIDE), and tools for calculating atom protusion (CX) and/or depth (DPX) indexes in 3D...
website       summary

ICM Web
The Interactive Chromatin Modeling (ICM) web server is an interactive tool that allows users to rapidly assess nucleosome stability and fold sequences of DNA into putative chromatin templates.
website       summary

iCR
Identify Conserved targets of a Regulon (iCR) predicts regulatory binding sites based on conservation across multiple species. The user provides an ungapped multiple sequence alignment representing the regulatory binding site...
website       summary

ICSNPathway
ICSNPathway is a web tool for the identification of candidate causal SNPs and their corresponding candidate causal pathways from genome wide association studies. ISCNPathway integrates linkage disequilibrium analysis, functio...
website       summary

IDconverter
IDconverter is a tool that converts gene, clone or protein IDs to other IDs which can be especially useful for microarray data analyses. This application is part of the suite Asterias.
website       summary

Idiographica
Idiographica is a general-purpose web application to build idiograms on-demand for human, mouse and rat. It allows users to generate high-quality idiograms with custom annotation according to their own genome-wide mapping/ann...
website       summary

IDT SciTools
IDT SciTools is a suite of online tools for the analysis and design of DNA and RNA oligomers. Tools include those for selection of PCR primers, antisense oligonucleotides, or sequences for RNA interference, as well as tools f...
website       summary

IEDB-3D
IEDB-3D is the 3D structural component of the Immune Epitope Database (IEDB). IEDB-3D catalogs B- and T-cell epitopes and Major Histocompatibility Complex (MHC) ligands for which 3D structures of complexes with antibodies, T-...
website       summary

IEDB-AR
The Immune Epitope Database Analysis Resource (IEDB-AR) is a collection of tools for the prediction and analysis of immune epitopes. Tools include B-cell and T-cell epitope prediction and epitope analysis tools. peptide:MHC-I...
website       summary

IGDD
Indian Genetic Disease Database (IGDD) is an integrated and curated repository of mutation data on common genetic diseases afflicting the Indian populations. Information on locus heterogeneity, type of mutation, clinical and ...
website       summary

IGG
Integration of Genotypes from Genechips (IGG) is a Java-based tool with graphic interface to integrate genotypes across high throughput genotyping platforms from Affymetrix and Illumina and the HapMap Project. It is equipped ...
website       summary

IGRhCellID
IGRhCellID is designed to integrate eight cell identification methods including seven methods (STR profile, gender, immunotypes, karyotype, isoenzyme profile, TP53 mutation and mutations of cancer genes) available in various ...
website       summary

i-GSEA4GWAS
i-GSEA4GWAS is a web server for identification of pathways and gene sets associated with traits. An improved gene set enrichment analysis (i-GSEA) is applied to genome wide association studies (GWAS).
website       summary

iHOP
iHOP (Information Hyperlinked over Proteins) allows researchers to explore a network of gene and protein interactions based on published scientific literature. For each gene search, iHOP reports sentences from abstracts assoc...
website       summary

IKMC
The International Knockout Mouse Consortium (IKMC) database and web portal serves as the central public web site for IKMC data. Researchers can access up-to-date information on IKMC knockout vectors, ES cells and mice for spe...
website       summary

ILM
Server which provides iterated loop matching and maximum weighted matching algorithms for pseudoknot containing RNA secondary structure prediction. Algorithms can apply thermodynamic and comparative information, and thus can ...
website       summary

IMCB - Fugu Genome Project
Lots of information on fugu including complete draft sequence, annotations, comparative vertebrate genomics, phylogenies, publications, and information about the fugu genome project; has some very useful tools including annot...
website       summary

IMEx
The IMEx consortium is a group of major public interaction data providers intending to share curation effort and exchange completed records on molecular interaction data, similar to successful global collaborations for protei...
website       summary

IMGT/3Dstructure
IMGT/3Dstructure-DB is the three-dimensional (3D) structure database of IMGT, the international ImMunoGenetics information system for immunogenetics and immunoinformatics. IMGT/3Dstructure-DB contains 3D structures of immunog...
website       summary

IMGT/HLA database
The IMGT/HLA database provides a searchable repository of highly curated HLA sequences. The naming of these HLA genes and alleles and their quality control is the responsibility of the WHO Nomenclature Committee for Factors o...
website       summary

IMGT/V-QUEST
The international ImMunoGeneTics information system (IMGT) V-QUEry and STandardization (V-QUEST) tool compares a user-provided fasta-formatted germline or rearranged T cell receptor or immunoglobulin variable sequence with a ...
website       summary

Immune Epitope Database
The Immune Epitope Database (IEDB) provides a catalog of experimentally characterized B and T cell epitopes, as well as data on Major Histocompatibility Complex (MHC) binding and MHC ligand elution experiments. The database r...
website       summary

iMODS
iMODS (Internal Coordinates Normal Mode Analysis Server) explores the colletive motions of proteins and nucleic acids using NMA in internal coordinates.
website       summary

iMOT
iMOT (interacting MOTif) server is designed to search for spatially interacting motifs among proteins sharing similar 3-dimensional structures.
website       summary

I-Mutant2.0
I-Mutant2.0 is a tool that can predict the effect of a single point mutation on protein stability from protein sequences or protein structures.
website       summary

INCLUSive
INCLUSive is a set of tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.
website       summary

INDELSCAN
INDELSCAN is a tool for genome-wide identification of indels.
website       summary

Influenza Virus Resources
Influenza Virus Resource presents data obtained from the NIAID Influenza Genome Sequencing Project as well as from GenBank, combined with tools for flu sequence analysis and annotation. In addition, it provides links to other...
website       summary

INFO-RNA
INFO-RNA is a server for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.
website       summary

inGAP-sv
inGAP-sv is a web server to identify and visualize structural variation from paired end mapping data. Several important features including local depth of coverage, mapping quality and associated tandem repeats are used to eva...
website       summary

InParanoid
The InParanoid project gathers proteomes of completely sequenced eukaryotic species plus Escherichia coli and calculates pairwise ortholog relationships among them. To facilitate data exchange and comparisons among ortholog d...
website       summary

Insignia
Insignia provides a web interface for identifying unique genomic signatures from a database of all current bacterial and viral genomic sequences. Input is any set of target and background genomes.
website       summary

In silico experiments with complete bacterial genomes
Provides tools for theoretical PCR amplification, AFLP-PCR and PFGE with all up-to-date public complete bacterial genomes (300+ genomes available).
website       summary

IntAct
IntAct is molecular interaction database and toolkit. Data is abstracted from the literature or from direct data depositions by expert curators following a deep annotation model providing a high level of detail. The search in...
website       summary

IntaRNA
IntaRNA is a program for the fast and accurate prediction of interactions between two RNA molecules. It has been designed to predict mRNA target sites for given non-coding RNAs (ncRNAs) like eukaryotic microRNAs (miRNAs) or b...
website       summary

INTEGRALL
INTEGRALL is a freely available, text-based search system developed to collect and organize information on integrons. There are more than 4800 integron sequences in the database.
website       summary

Integrated Microbial Genomes (IMG)
The integrated microbial genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG contains both draft and complete microbial genomes...
website       summary

IntEnz: Integrated relational Enzyme database
The goal of IntEnz is to create a single relational database containing enzyme data from three different sources: The Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the n...
website       summary

INTERFEROME
INTERFEROME is an open access database of types I, II and III Interferon regulated genes collected from analysing expression data sets of cells treated with IFNs. This database integrates expression information with annotatio...
website       summary

Intergr8
Integr8 is a browser for information relating to completed genomes and proteomes. It provides access to species descriptions, literature, statistical analysis and summary information about each complete proteome; and integrat...
website       summary

InterMine
InterMine is an open source data warehouse built specifically for the integration and analysis of complex biological data. InterMine enables the creation of biological databases accessed by sophisticated web query tools.
website       summary

International HapMap Project
The haplotype map, or HapMap, is a tool that will allow researchers to find genes and genetic variations that affect health and disease.
website       summary

International Nucleotide Sequence Database Collaboration
International Nucleotide Sequence Database Collaboration (INSDC) public domain nucleotide sequence is captured, preserved and presented. The partners of this long-standing collaboration work closely together to provide data f...
website       summary

International Society for Computational Biology
Scholarly society dedicated to advancing the scientific understanding of living systems through computation; emphasis is on the role of computing and informatics in advancing molecular biology.
website       summary

Interolog/Regulog Database
Database of protein orthologs that interact (interologs) and proteins with conserved regulatory relationships across species (regulogs). Contains data for C. elegans, Drosophila, Arabidopsis, and Yeast.
website       summary

InteroPORC
InteroPorc is an automatic prediction tool to infer protein-protein interaction networks. It is applicable for any species present in the Integr8 database (more than 1500 organisms). The method combines known interactions and...
website       summary

InterPro
Integrated database of commonly used signature databases (e.g. PROSITE, PRINTS, SMART, Pfam, ProDom); text- and sequence-based searches.
website       summary

InterProScan
InterProScan allows you to query using different protein signature recognition methods to look up InterPro annotations for your sequence. These annotations results often include gene ontology terms that you can associate with...
website       summary

IntFOLD
The IntFOLD web server is an integrated web resource for protein folding recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.
website       summary

INTREPID
The INTREPID web server predicts functionally important residues in proteins such as catalytic residues. Users input protein sequence. Residues predicted to be functionally important are displayed on homologous 3D structures ...
website       summary

iPath
iPath is a web tool for the visualization and analysis of cellular pathways. Its primary map summarizes the metabolism in biological systems.
website       summary

iPBA
iPBA uses specialized protein block substitution matrices and anchor based methodology for pairwise protein structure comparisons.
website       summary

IPD
The Immuno Polymorphism Database (IPD) is a set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and c...
website       summary

iPDA
iPDA (Integrated Protein Disorder Analyzer) predicts disordered regions of a query protein sequence.
website       summary

IPI - International Protein Index
IPI provides a top level view of the human, mouse and rat proteome data found in Swiss-Prot, TrEMBL, RefSeq and Ensembl.
website       summary

iRefIndex
iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index allows the user to search f...
website       summary

IRESite
The IRESite presents carefully curated experimental evidence of many eukaryotic viral and cellular internal ribosome entry site (IRES) regions. The IRESite tool provides biologically meaningful information regarding the IRESs...
website       summary

iSARST
iSARST is a web server for protein structural similarity searches. It is a batch-processing and integrated implementation of several structural comparison tools and database search methods.
website       summary

ISC Large-scale Sequencing Project Database
The International Sequencing Consortium (ISC) Large-scale Sequencing Project Database contains information on current and completed sequencing projects, including project timelines, funding agencies, sequencing strategy and l...
website       summary

ISfinder
ISfinder is a dedicated insertion sequence (IS) database which assigns names to individual ISs to maintain a coherent nomenclature, an IS repository including >3000 individual ISs from both bacteria and archaea and provides a...
website       summary

IslandPath
IslandPath aids genomic island detection in prokaryotic genome seqeunces, using features such as dinucleotide bias, G+C, location of tRNA genes, annotations of mobility genes, etc. Genomic islands are defined here as genomic ...
website       summary

IsoBase
IsoBase is a database identifying functionally related proteins across five major eukaryotic model organisms: yeast, fly, worm, mouse, and human. Clusters were computed using the IsoRankN algorithm, which uses spectral method...
website       summary

IsoFinder
IsoFinder is a tool for the prediction of isochores for a user-supplied sequence.
website       summary

ISOTOPICA
Tools developed to aid in the identification of mass spectrum that allow the calculation of mass values with isotopic distributions based on molecular formulas, peptides/proteins, DNA/RNA, carbohydrate sequences or combinatio...
website       summary

ISPIDER Central
The ISPIDER Central provides a range of services for integrative data analysis in mass spectrometry-based proteomics. It enables users to query multiple proteomic repositories and to add information to proteins retrieved from...
website       summary

iSPOT
iSPOT (Sequence Prediction Of Target) uses experimental interaction data combined with structural residue-residue contact information to predict the peptide binding specificity of SH3, PDZ, and WW domains.
website       summary

ISTECH SNPAnalyzer
ISTECH SNPAnalyzer is a tool for the statistical analysis of SNP data that includes Hardy Weinberg equilibrium (HWE), haplotype estimation, linkage disequilibrium (LD), and QTL analyses. Registration required; some browser re...
website       summary

iTOL
The Interactive Tree of Life (iTOL) tool is useful for the display, manipulation and annotation of phylogenetic trees. In addition to standart tree viewer functions, it offers powerful annotation of phylogenetic trees with va...
website       summary

ITS2
The Internal Transcribed Spacer 2 Database (ITS2) includes a homology based RNA structure prediction algorithm which allows the detection and secondary structure prediction of ITS2 sequences. This resource also contains more ...
website       summary

ITS2
The ITS2 Database holds information about sequence, structure and taxonomic classification of all internal transcribed spacer 2 (ITS2) in GenBank. ITS2 can now be searched with a modified BLAST considering both sequence and s...
website       summary

IUPHAR-DB
The IUPHAR database is an online reference resource for classes of human drug targets and related proteins. As well as providing recommended nomenclature, the database integrates information on the chemical, genetic, function...
website       summary

JASPAR
JASPAR is a non-redundant, curated collection of transcription factor binding profiles. Each profile is generated from published, experimentally defined eukaryotic transcription factor binding sites.
website       summary

JASPAR
JASPAR is an open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific manner. The database now holds 457 non-red...
website       summary

java.sun.com
The source for java technology.
website       summary

The Java Tutorial
The place to go for your first cup of Java.
website       summary

JCat
JCAT (Java Codon Adaptation Tool) is a tool that can adjust the codon usage of an input sequence to the selected organism. Useful for improving the expression of foreign genes in hosts with different codon usage.
website       summary

JEvTrace
Jevtrace is a tool that combines multiple sequence alignments, phylogenetic, and structural data for identification of functional sites in proteins.
website       summary

Joes Site - Phylogeny Programs
Comprehensive list of phylogeny packages, compiled by Joe Felsenstein, creator of Phylip.
website       summary

JOY
JOY is a program for displaying 3D structural information in a multiple sequence alignment.
website       summary

jpHMM
Jumping Profile Hidden Markov Model (jpHMM) takes a HIV-1 or HBV genome sequence and uses a pre-calculated multiple alignment of the major HIV-1 or HBV subtypes to predict the phylogenetic breakpoints and HIV/HBV subtype of t...
website       summary

Jpred 3
Jpred 3 is an improved web server for predicting protein secondary structure in three states (alpha helix, beta strand and coil). Improvements include better usability, batch submission of sequences and updates to the search ...
website       summary

jPREdictor
jPREdictor predicts cis-regulatory elements using short motifs that are known to bind regulatory proteins. Predictions are made by searching for clusters of these motifs, and weighting these clusters by applying a positive or...
website       summary

JProGO
JProGO is a tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information.
website       summary

JVirGel
JVirGel creates a virtual 2-D gel based on theoretical molecular weights and calculated isoelectric points from a set of input proteins or proteomes.
website       summary

K2N
K2N is a web service to get from knotted to nested RNA structures. This site provides access to a variety of methods for pseudoknot removal.
website       summary

KAAS
KAAS (KEGG Automatic Annotation Server) is a tool for ortholog assignment and pathway mapping. KAAS provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result con...
website       summary

Kalign, Kalignvu, and Mumsa
Kalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences. Kalignvu is an xml based alignment viewer that allows users to resize alignments and choose different c...
website       summary

KaPPA-View4
KaPPA-View4 is a metabolic pathway database which is able to overlay gene-to-gene and/or metabolite-to-metabolite relationships as curves on a metabolic pathway map, or on a combination of up to four maps. Pathway maps of the...
website       summary

KARMA
KARMA (Keck Array Manager and Annotator) allows you compare and annotate your own microarrays against other available arrays. Comparison of arrays can be achieved within the same species as well as across species (array compa...
website       summary

KEGG
The KEGG PATHWAY database contains pathway maps for the molecular systems in both normal and perturbed states. In the KEGG DISEASE database, each disease is represented by a list of known disease genes, any known environmenta...
website       summary

KEGG: Kyoto Encyclopedia of Genes and Genomes
Pathway maps, molecular catalogs, genome maps and gene catalogs that capture knowledge about interactions in terms of information pathways. KEGG comprises several databases, including BRITE (protein-protein interactions), PAT...
website       summary

KFC Server
The KFC Server is a web-based implementation of the Knowledge-based FADE and Contacts (KFC) model. KFC predicts the subset of residues responsible for the majority of a protein interface's binding free energy. Users inpu...
website       summary

KINARI-Web
KINARI-Web is a web server for performing rigidity analysis and visually exploring rigidity properties of proteins. It also provides tools for pre-processing the input data, such as selecting relevant chains from PDB files, a...
website       summary

KinasePhos
KinasePhos is a tool for identifying kinase-specific phosphorylation sites in protein sequences.
website       summary

KinasePhos 2.0
KinasePhos 2.0 is a new version of a kinase-specific phosphorylation site prediction tool.
website       summary

KinDOCK
KinDOCK is a tool for the analysis of ATP-binding sites of protein kinases based on a structural library of protein kinase-ligand complexes extracted from the Protein Data Bank (PDB).
website       summary

Kinefold
Kinefold calculates (and animates) the folding kinetics of RNA sequences including pseudoknots.
website       summary

kmacs
The k Mismatch Average Common Substring (k-macs) web server provides alignment-free sequence comparison. kmacs uses a distance measure based on inexact substring matches.
website       summary

Knoppix
Knoppix is a GNU/Linux distribution that boots and runs completely from cd. It includes recent linux software and desktop environments, with programs such as OpenOffice.org, Abiword, The Gimp, Konqueror, Mozilla, and hundreds...
website       summary

KNOTS
KNOTS is a web server that detects knots in protein structures.
website       summary

KOBAS
KEGG Orthology-Based Annotation System (KOBAS) annotates sequences with KEGG Orthology terms and identifies the frequently occurring (or significantly enriched) pathways among the queried sequences compared against a backgrou...
website       summary

KUPS
KUPS (The University of Kansas Proteomics Service) provides protein-protein interaction (PPI) data. It allows users to construct ready-to-use data sets of interacting protein pairs (IPPs), non-interacting protein pairs (NIPs)...
website       summary

LAGAN
The LAGAN alignment toolkit consists of components: CHAOS (a pairwise local aligner optimized for non-coding, and other poorly conserved regions of the genome.), LAGAN (a highly parametrizable pairwise global alignment progra...
website       summary

Laminin database
The Laminin(LM)-database is a database focusing on the non-collagenous extracellular matrix protein family, the LMs. The homepage is subdivided into LMs, receptors, extracellular binding and other related proteins. Each tab o...
website       summary

Learn how to use NCBI resources
Seven interrelated modules expose the user to tools and databases currently used by researchers in molecular biology.
website       summary

Life Science Directory
Extensive list of links to biology resources; compiled by Amos Bairoch of SWISS-PROT.
website       summary

LINCS Canvas Browser (LCB)
LINCS (Library of Integrated Network-based Cellular Signatures) is an interactive web server to query, browse and interrogate LINCS L1000 gene expression signatures.
website       summary

Links to the Genetic World
Large directory of online resources.
website       summary

Linux.com
This site has great tutorials and links to other linux sites, supported by the OSDN.
website       summary

The Linux Cookbook
Tips and techniques for everyday use.
website       summary

Linux DistroWatch
This site is an attempt to provide a basic feature list and a package comparison table of major, minor and regional Linux distributions. It is updated daily with news from the Linux distribution world.
website       summary

Linux Documentation Project
The Linux Documentation Project is a repository of Linux documentation including documents about individual software, HOWTO documents, FAQs, and more.
website       summary

Linux Online
Comprehensive information and resources about the Linux Operating System.
website       summary

LIPID MAPS
LIPID Metabolites And Pathways Strategy (LIPID MAPS) is a consortium that presents a collection of tools for performing tasks such as drawing lipid structures and predicting possible structures from mass spectrometry data.
website       summary

A List of Bioinformatics Courses
A list of programs, workshops and individual courses in bioinformatics maintained at the Robert S. Boas Center for Genomics and Human Genetics.
website       summary

LitInspector
A literature search tool providing gene homonym mining within the PubMed database. Search terms are highlighted in the results. LitInspector also performs signal transduction pathway mining using a manually curated database o...
website       summary

LitMiner
LitMiner is a literature data mining tool that is based on the annotation of key terms in article abstracts followed by statistical co-citation analysis of annotated key terms in order to predict relationships between genes, ...
website       summary

lncRNAdb
lncRNAdb database contains a comprehensive list of long noncoding RNAs (lncRNAs) that have been shown to have, or to be associated with, biological functions in eukaryotes, as well as messenger RNAs that have regulatory roles...
website       summary

Loc3D
LOC3D is a database of predicted subcellular localization for eukaryotic proteins of known three-dimensional (3D) structure and includes tools to predict the subcellular localization for submitted protein sequences.
website       summary

Localizome
Localizome predicts transmembrane (TM) helix number and topology for eukaryotic proteins using protein domain information.
website       summary

LocalMove
LocalMove is a web server for computing on-lattice fits for biopolymersusing input from PDB files for proteins or RNA molecules. Results are output in PDB file format and include a 3D movie of the intermediate conformations s...
website       summary

LOCATE
LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of mouse proteins.
website       summary

LocDB
LocDB is a manually curated database with experimental annotations for the subcellular localizations of proteins in Homo sapiens (HS, human) and Arabidopsis thaliana (AT, thale cress). Each database entry contains the experim...
website       summary

LOCtarget
LOCtarget is a tool for predicting, and a database of pre-computed predictions for, sub-cellular localization of eukaryotic and prokaryotic proteins. Several methods are employed to make the predictions, including text analys...
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LocTree 3
LocTree3 is a web server for protein subcellular localization prediction.
website       summary

LogoBar
LogoBar is a Java application to display protein sequence logos. With this application you can generate protein sequence logos from multiple sequence alignments that show the amino acid incidence at every position.
website       summary

LOVD
The Leiden Open (source) Variation Database (LOVD) To provides a flexible, freely available tool for the gene-centered collection and display of DNA variations.
website       summary

LowComplexity
LowComplexity is a tool that searches for low complexity regions of DNA or protein sequences. Using LowComplexity you can search long sequences (chromosomes, genomes) or a set of aligned sequences. This resource also contains...
website       summary

LSD
This database contains senescence associated genes (SAGs) from 21 species retrieved based on genetic, genomic, proteomic, physiological or other experimental evidence, and classified into different categories according to the...
website       summary

LTR_Finder
LTR_Finder (Long Terminal Repeat Finder) is an efficient program for finding full-length LTR retrotransposons in genome sequences.
website       summary

Lynx
Lynx Web Services provides programmatic access to the analytical tools (Enrichment Analysis, and Network-based gene prioritization) and annotations on the genes (integrated from over 35 databases).
website       summary

M4T
M4T (Multiple Mapping Method with Multiple Templates) is a comparative protein structure modeling server that uses a combination of multiple templates and iterative optimization of alternative alignments.
website       summary

MADAP
MADAP is a clustering tool for the interpretation annotation data mapped onto complete or partial genome sequences. Initially developed for determining transcription start sites (TSS) by defining 5\' and 3\'ends of ...
website       summary

MADNet
Microarray Database Network (MADNet) is a data mining and visualization tool for analysis of diverse high-throughput biological data such as microarrays and phage display experiments. Data is integrated with information from ...
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MAGIA2
miRNA and Genes Integrated Analysis (MAGIA2) is a web tool for the integrative analysis of in silico target prediction, and reconstruction of post-transcriptional regulatory and mixed regulatory networks from miRNA and gene e...
website       summary

MagicViewer
MagicViewer allows easy visualization of short read mapping, and identification and annotation of genetic variation using next-generation sequencing data. Platforms covered include Roche 454, ABI SOLiD and Illumina.
website       summary

MAGIIC-PRO
MAGIIC-PRO is a tool for detecting patterns in protein sequences. MAGIIC-PRO takes a protein sequence as input and helps users prepare training data for the pattern mining experiments by using Swiss-Prot annotations or by PSI...
website       summary

MAGMA
MAGMA can be used for the analyses of two-channel microarray experiments and computes genes with significant differential expression using R and Bioconductor. Automatically generated R-scripts are available for download.
website       summary

MAGNOLIA
MAGNOLIA is software for multiple alignment of protein coding and structural RNA sequences making use of the putative functions of these sequences. Magnolia extracts information from the similarities and differences in the da...
website       summary

Maize Genetics and Genomics Database
A central repository for public maize information.
website       summary

MaM
The Multiple alignment Manipulator (MaM) takes a multiple alignment of genomic sequences as input and calculates the locations of exons, common repeat elements and unique regions based on user-selected programs/information. T...
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Mammalian Gene Collection
Goal is to provide a complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for human and mouse; publicly accessible.
website       summary

MAPPIS
Multiple Alignment of Protein-Protein Interfaces (MAPPIS) is a tool for the recognition of spatially conserved chemical interactions shared by a set of protein-protein interfaces or regions of protein interaction. Users input...
website       summary

MARBL
MARBL is an open-source package for indexing the text components of GenBank records and the NLM article abstracts associated with them. A few demonstrations of the package are also available at this website.
website       summary

MarkUs
MarkUs is a web server for analysis and comparison of the structural and functional properties of proteins.
website       summary

MARQ
MARQ is a web based application that allows users to compare a query set of genes (query signature) against a gene signature database built from GEO datasets for different organisms and platforms.
website       summary

MartView
The Ensembl EnsMart Genome Browser (MartView) is a tool for data retrieval and data mining that integrates data from Ensembl. Through the web interface MartView allows you to apply a series of filters to create custom dataset...
website       summary

MASCOT (Matrix Science)
Protein identification by peptide mass; excellent documentation; incorporates code from MOWSE but allows more search methods on more sequence databases.
website       summary

MassNet
MassNet web server provides comprehensive functional annotation of mass spectrometry data. Annotation includes physico-chemical analysis, KEGG pathway assignment, GO mapping, and protein-protein interaction prediction.
website       summary

MassTRIX
With applications in metabolomics and other mass spectrometry studies, MassTRIX is a hypothesis driven approach to the annotation of mass spectrometry data. Data is output in context on a KEGG pathway map.
website       summary

massXpert
massXpert is a proteomics-oriented program mainly concerned with protein physico-chemistry and protein/peptide mass spectra simulations.
website       summary

Match
Match is a weight matrix-based tool which searches for putative transcription factor binding sites (TFBS) in DNA sequences. Registration at the site is free and is required to use Match.
website       summary

MatchMiner
MatchMiner is a tool to compare and convert gene identifiers. Users can translate single or lists of identifiers from one form to another, or compare two lists of identifiers for common gene references.
website       summary

MATRAS
MATRAS is a resource for comparing protein three dimensional (3D) structures. Users can compare protein 3D structures using pairwise alignments, multiple alignments, or by a comparing against a library of known structures.
website       summary

MatrixDB
MatrixDB is a database focused on interactions established by extracellular proteins and polysaccharides. MatrixDB takes into account the multimeric nature of several extracellular protein families for the curation of interac...
website       summary

MaxAlign
MaxAlign is a web server for maximizing usable data in an alignment. It maximizes the number of nucleotide (or amino acid) symbols present in gap-free columns by selecting the optimal subset of sequences to exclude from the a...
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MaXIC-Q
The MaXIC-Q web server performs various quantification analyses on large-scale datasets generated from proteomics studies using isotope labeling. For input MS data, output is given in projected ion mass spectrum and extracted...
website       summary

McGill Centre for Bioinformatics
The Centre for Bioinformatics at McGill is committed to developing the area as a focus of academic research excellence.
website       summary

McPromoter
The Markov Chain Promoter Prediction Server (McPromoter) uses statistics to predict eukaryotic DNA transcription start sites.
website       summary

MDscan
Server designed to pinpoint protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites.
website       summary

Medical Acronym Finder
The acronym database provides free access to medical/biological acronyms. It has 100,000+ acronyms and the users can also contribute by rating the entries quality. In the backend, it is generated from medline data.
website       summary

MedlineRanker
The MedlineRanker web server allows a flexible and fast ranking of Medline abstracts for a topic of interest without expert knowledge.
website       summary

MedMiner
MedMiner can be used to select genes from a microarray set based on GeneCards information. Based on the genes selected one can then search PubMed abstracts using known gene synonyms and other user-specified search parameters....
website       summary

MEDock
MEDock (Maximum-Entropy based Docking) is a tool for predicting ligand binding sites.
website       summary

MEGA
MEGA (Molecular Evolutionary Genetics Analysis) is a software package for phylogenetic analysis with a graphical user interface. It allows viewing and editing of the aligned input sequence data and provides many tools for phy...
website       summary

Megx.net
Megx.net is a database and portal that provides integrated access to georeferenced marker genes, environment data and marine genome and metagenome projects for microbial ecological genomics. All data are stored in the Microbi...
website       summary

MelinaII
MelinaII (Motif Elucidator in Nucleotide Sequence Assembly) can run multiple motif prediction tools (Consensus, MEME, Gibbs Sampler, MDScan, Weeder) simultaneously. Graphical results can be used to compare predictions of pote...
website       summary

MEME Suite
The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein da...
website       summary

MeMo
Methylation Modification Prediction Server (MeMo) is a server that predicts arginine and lysine sites that undergo methylation using a support vector machine (SVM).
website       summary

MeMotif
MeMotif is a database and wiki which collects more than 2000 known and novel computationally predicted linear motifs in alpha-helical transmembrane proteins. Motifs are fully described in terms of several structural and funct...
website       summary

MemPype
MemPype is a Python-based pipeline that integrates several tools for the prediction of topology and subcellular localization of Eukaryotic membrane proteins.
website       summary

The Mendel Site
The Mendel Site contains a collection of tools for predicting lipid postranslational modifications and localization signals in protein sequences.
website       summary

MEROPS
The MEROPS database is a collection of peptidases. The database has a hierarchical classification in which homologous sets of peptidases and protein inhibitors are grouped into protein species, which are grouped into families...
website       summary

mESAdb
microRNA expression and sequence analysis database (mESAdb) is a database for the multivariate analysis of sequences and expression of microRNAs from multiple taxa. mESAdb is coupled with statistical analysis and visualizatio...
website       summary

Mesquite
Mesquite is an open source software project designed to deal with comparative data about organisms and evolutionary analyses. Mesquite contains modules for phylogenetic analysis, population genetics, and non-phylogenetic mult...
website       summary

MET
The Motif Enrichment Tool (MET) takes user-defined gene sets and identifies significantly associated sets of genes that share a regulatory motif. The tool is available for a number of model organisms (human, mouse, zebrafinc...
website       summary

Meta-BASIC
Meta-BASIC is a tool for detecting distant homologues using meta-profiles which combine both sequence positional variability and secondary structure.
website       summary

MetaBioME
MetaBioiME is a web resource to find novel homologs for known Commercially Useful Enzymes (CUEs) in metagenomic datasets and completed bacterial genomes.
website       summary

MetaboAnalyst 2.0
MetaboAnalyst is a web-based pipeline for metabolomic data processing, statistical analysis and functional interpretation. It performs data processing and normalization for various metabolomic data types. It provides various ...
website       summary

MetaCyc
The MetaCyc database is a comprehensive resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the p...
website       summary

MetalDetector
MetalDetector identifies CYS and HIS involved in transition metal protein binding sites beginning with protein sequence alone. The geometry of the metal binding site is also predicted.
website       summary

Meta-MEME
Creates hidden Markov model of motif from MEME output and searches sequence database for matches to this motif.
website       summary

MetaMHC
MetaMHC integrates the outputs of leading MHC binding predictors. MHC class I and II peptides binding are predicted.
website       summary

MetaPath Online
MetaPath Online gives users access to an algorithm for network expansion. Starting with given metabolites, called seed compounds, the algorithm uses known information about metabolic reactions and pathways to expand the netwo...
website       summary

metaSHARK
Metabolic Search And Reconstruction Kit (metaSHARK) provides an interactive visualisation platform for the KEGG metabolic network in the form of the SHARKview applet.
website       summary

MetExplore
MetExplore is a web tool that links metabolites identified in untargeted metabolomics experiments within the context of genome-scale metabolic networks. Metabolomics data is mapped onto the specific metabolic network of an or...
website       summary

Mfold
Predict RNA secondary structure from sequence; does not predict pseudoknots - see PKNOTS.
website       summary

mGene.web
mGene.web is a web server for the genome wide prediction of protein coding genes from eukaryotic DNA sequences based on pre-computed models of gene structures. Users may also compute their own model using their own data.
website       summary

mGenomeSubtractor
mGenomeSubtractor performs mpiBLAST-based comparison of reference bacterial genomes against multiple user-selected genomes. Such in silico subtractive hybridization also allows for definition of species-specific gene pools an...
website       summary

MGIP
The Meningococcus Genome Informatics Platform (MGIP) is a suite of computational tools for the analysis of multilocus sequence typing data. Input DNA sequence files are analyzed to provide allele calls, and to characterize th...
website       summary

MIAMExpress
MIAME (minimum information about a microarray experiment) compliant microarray data submission tool.
website       summary

Michael Smith Genome Sciences Centre
Deploy resources and technology of a high-throughput genome mapping and DNA sequencing lab to decrypt the genetic code, specifically to advance cancer research, diagnosis, and treatment.
website       summary

MICheck
MICheck (Microbial Genome Checker) allows the user to verify gene annotations in previously published microbial genomes.
website       summary

Microarray Gene Expression Database
Group facilitating the development of an international repository for gene expression data and the experimental and database standards required for such an endeavour.
website       summary

Microarray Retriever
Microarray Retriever (MaRe) is a web tool that enables batch search and retrieval of microarray datasets matching user specified criteria from the data in GEO and ArrayExpress microarray repositories. Such batch download faci...
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Microbe Browser
The Microbe Browser is a web server providing comparative microbial genomics data integrated from GenBank, RefSeq, UniProt, InterPro, Gene Ontology and the Orthologs Matrix Project (OMA) databases. Gene predictions based on 5...
website       summary

MicrobesOnline
MicrobesOnline portal includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms. MicrobesOnline includes a comparative genome browser based on phylogenet...
website       summary

Microbial Genome Database (MBGD)
The microbial genome database (MBGD) for comparative analysis is a platform for microbial comparative genomics based on automated ortholog group identification. A prominent feature of MBGD is that it allows users to create or...
website       summary

Microbial Genome Viewer
Tool for visualization of microbial genomes. Chromosome wheels and linear genome maps with user specified features/color coding can be generated interactively. Graphics are created in SVG format.
website       summary

MicroFootPrinter
MicroFootPrinter identifies the conserved motifs in regulatory regions of prokaryotic genomes using the phylogenetic footprinting program FootPrinter.
website       summary

MicroInspector
MicroInspector is a tool that detects miRNA (microRNA) binding sites in your input sequence by searching against databases of known miRNA binding sites.
website       summary

MiCroKit
MiCroKit database of proteins that localize in midbody, centrosome and/or kinetochore. The MiCroKit database contains experimentally verified microkit proteins from the scientific literature that have unambiguous supportive e...
website       summary

MIDAW
MIDAW (MIcroarray Data Analysis Web tool) is a data normalization and analysis tool for microarray data.
website       summary

MIGenAS Toolkit
Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and pr...
website       summary

MinActionPath
MinActionPath calculates the most-probable trajectory between two known structural states of a protein.
website       summary

MINT
MINT is a public repository for molecular interactions reported in peer-reviewed journals. MINT has adopted the PSI-MI standards for the annotation and for the representation of molecular interactions and is a member of the I...
website       summary

miPred
miPred (microRNA Predictor) can distinguish between real and pseudo microRNA precursors.
website       summary

MIPS
Munich Information Centre for Protein Sequences projects include: fungal genome analysis, plant genome bioinformatics, structural genomics, proteomics and genome annotation. Projects and databases include: CYGD, MNCDB, NGFN, ...
website       summary

MIPS
The Munich Information Center for Protein Sequences (MIPS) provides annotated collections of biological data. High-quality reference resources include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genom...
website       summary

mirAct
mirACT web server is a tool designed to investigate miRNA activity in gene expression data. It uses the negative regulation relationship between miRNAs and their target genes.
website       summary

miRanalyzer
miRanalyzer is a web server tool for the analysis of high throughput sequencing experiments for microRNAs. Users input a list of unique reads and copy number. The tool detects all known microRNA sequences annotated in miRBase...
website       summary

miRBase
miRBase is a repository for all microRNA sequences and annotation. miRBase has mapped reads from short RNA deep-sequencing experiments to microRNAs in miRBase and developed web interfaces to view these mappings. The user can ...
website       summary

mirConnX
mirConnX is a web server for inferring, displaying and parsing mRNA and microRNA gene regulatory networks. mirConnX combines sequence information with gene expression data analysis to create a disease specific, genome wide re...
website       summary

miRGator v2.0
miRGator is an integrated database of microRNA (miRNA)-associated gene expression, target prediction, disease association and genomic annotation for the functional investigation of miRNA. miRGator v2.0 contains information ab...
website       summary

miRGen
miRGen 2.0 is a database that aims to provide comprehensive information about the position of human and mouse microRNA coding transcripts and their regulation by transcription factors, including a unique compilation of both p...
website       summary

miRTarBase
miRTarBase database contains miRNA-target interactions (MTIs). The collected MTIs are validated experimentally by reporter assays, western blot, or microarray experiments with overexpression or knockdown of miRNAs.
website       summary

mirTools
mirTools allows users to comprehensively characterize the small RNA transcriptome from high-throughput sequencing data. Users can filter quality reads, align short reads to the reference genome, classify small RNA candidates ...
website       summary

miRU
miRU is a tool that takes as an input a small miRNA sequence and then searches for complementary matches in TIGR plant-specific gene data sets to predict potential target genes.
website       summary

MIRU-VNTRplus
MIRU-VNTRplus allows users to analyze genotyping data of their Mycobacterium tuberculosis strains either alone or in comparison with the reference DB of strains. The web server also includes tools to search for similar strain...
website       summary

miRvestigator
miRvestigator is a web based tool to identify miRNAs mediating co-regulation of gene expression patterns observed in transcriptome profilng data. The miRvestigator takes as input a list of co-expressed genes and returns the m...
website       summary

MirZ
MirZ is a web server that for evaluation and analysis of miRNA. It integrates two miRNA resources: the smiRNAdb miRNA expression atlas and the E1MMo miRNA target prediction algorithm.
website       summary

MiST
The MiST2 database identifies and catalogs the repertoire of signal transduction proteins in microbial genomes. These are identified by searching protein sequences for specific domain profiles that implicate a protein in sign...
website       summary

MitoGenesisDB
MitoGenesisDB focuses on the dynamic of mitochondrial protein formation through global mRNA analyses. Three main parameters confer a global view of mitochondrial biogenesis: (i) time-course of mRNA production in highly synchr...
website       summary

MIT OpenCourseWare
MIT OpenCourseWare provides free and open access to some of MIT\'s course materials. There are hundreds of courses represented from over thirty different disciplines, including Biology, Health Sciences and Technology, and Sci...
website       summary

MITOPRED
MITOPRED uses Pfam domains, pI values and amino acid composition to predict nuclear-encoded mitochondrial proteins. Predictions have been precomputed for a number of proteomes, as well as for all Eukaryotic sequences in Swiss...
website       summary

MKT
Standard and Generalized McDonald-Kreitman Test (MKT) is a web tool for the molecular level detection of signatures of natural selection.
website       summary

MLST
MLST (Multi Locus Sequence Typing) is a nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms using the sequences of internal fragments of seven house-keeping gene...
website       summary

MMDB
Molecular Modelling Database of 3-D structures; experimentally determined structures only.
website       summary

MMIA
microRNA and mRNA Integrated Analysis (MMIA) is a web server that integrates miRNA and mRNA expression data with predicted miRNA target information. MMIA incorporates miRNA prediction algorithms (TargetScan, PITA, PicTar).
website       summary

MobilomeFINDER
MobilomeFINDER (Mobile Genome FINDER) is a tool for high-throughput genomic island discovery.
website       summary

ModBase
ModBase is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment...
website       summary

Modeller
Homology or comparative modeling of 3D protein structures.
website       summary

ModelTest Sever
ModelTest is program for the selection the model of DNA evolution (nucleotide substitution) that best fits your data from phylogenetic analyses.
website       summary

MODEST
MODEST: A web-based tool for rapid and effective design of optimal multiplex automated genome engineering (MAGE) oligos based on simple input, to achieve any mutation possible with MAGE. The tool is useful in oligonucleotide-...
website       summary

MODi
Modi is a tool that facilitates the interpretation of tandem mass spectra in order to identify post-translational modifications (PTMs) in a peptide.
website       summary

MODPROPEP
MODPROPEP is a server for structural modeling of protein kinases and MHC proteins in complex with their substrate peptides.
website       summary

MoD Tools
Tools for Motif Discovery (MoD) in nucleotide sequences that includes: Weeder, a program for detecting transcription factor binding sites (TFBS) in coregulated genes; WeederH, a tool for detecting TFBS and regulatory regions ...
website       summary

MolAxis
The MolAxis web server allows users to identify transmembrane channels in proteins and channels in macromolecules that connect buried cavities to the external surface. Gating residues, channel lining residues and a 3D graphic...
website       summary

MolLoc
Molecular Local surface comparison (MolLoc) is a web server for the structural comparison of molecular surfaces. Users input two structures in PDB format for comparison of binding sites, cavities or other residues.
website       summary

MolMovDB
The Database of Macromolecular Movements (MolMovDB) contains a collection of animated protein and RNA structures to assist in the exploration of macromolecular flexibility. Software for structure analysis is also available.
website       summary

MolProbity
MolProbity is a structure validation web service for diagnosing problems in 3D models of proteins, nucleic acids or complexes. It adds and optimizes H atoms (correcting 180° flipped Asn/Gln/His sidechains), and then calculat...
website       summary

MolSurfer
Molsurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures. It can be used to study protein-protein and protein-DNA/RNA interfaces.
website       summary

MONSTER
MONSTER takes a PDB structure file as input, and predicts non-bonding interactions that have the potential to provide stability to the molecule. The output can be viewed or downloaded as XML or text, or can be viewed as a 3D ...
website       summary

Montreal Proteomics Network (RPMPN)
A network of researchers working towards the identification, characterization and localization of every protein for every mammalian cell organelle.
website       summary

MORPHIN
MORPHIN is a web-based bioinformatics tool to study human diseases using model organism genes. MORPHIN harnesses model organisms to investigate human diseases by projecting information from model organism studies on a human i...
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Motif3D
Motif3D is a protein structure viewer for visualizing sequence motifs contained in the PRINTS database on 3D structures.
website       summary

MotifViz
MotifViz is a tool for detecting overrepresented transcription factor binding motifs. Four motif discovery programs are accessible from the MotifViz web interface: Clover, Rover, Motifish and Possum.
website       summary

MotiveValidator
MotiveValidator is a web server for a set of applications designed to help you determine whether a residue or a ligand in a biomolecule or biomolecular complex is structurally complete and correctly annotated according to its...
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Mouse Atlas of Gene Expression
A quantitative and comprehensive atlas of gene expression in mouse development. The project has a goal of producing 150 publically available SAGE libraries.
website       summary

Mousebook
The MouseBook databases and web portal provide access to information about mutant mouse lines held as live or cryopreserved stocks at MRC Harwell. The MouseBook portal integrates curated information from the MRC Harwell stock...
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Mouse Genetics: Concepts and Applications
Online version of textbook by Lee Silver.
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Mouse Genome Database (MGD)
The Mouse Genome Database (MGD) is the community model organism database for the laboratory mouse and the source for phenotype and functional annotations of mouse genes. MGD includes a complete catalog of mouse genes and geno...
website       summary

MouseIndelDB
MouseIndelDB is an integrated database resource containing thousands of previously unreported mouse genomic indel (insertion and deletion) polymorphisms ranging from approximately 100 nt to 10 Kb in size. The database current...
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Mouse Resources
Linked list of major mouse genome and mutation resources; maintained by the Trans-NIH Mouse Initiative.
website       summary

MovieMaker
MovieMaker is a web server that accepts PDB files or PDB accession numbers as input and allows short (~10 sec) downloadable movies to be generated of protein motions and interactions.
website       summary

MoViES
MoViES (Molecular Vibrations Evaluation Server) allows the computation of the vibrational and thermal fluctuations dynamics for the chemical bonds of biomolecules. The server takes as input a structure file in PDB format and ...
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MOWServ
MOWServ provides integrated access to databases and analytical tools. Based on the BioMoby protocol for inter-service communication.
website       summary

MPI Toolkit
Max-Planck Institute Bioinformatics Toolkit provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein str...
website       summary

MPlot
MPlot is a web server for the analysis, visualization and plotting of the tertiary structure contacts and geometrical features of helical membrane proteins.
website       summary

MPromDb update 2010
MPromDb (Mammalian Promoter Database) is a curated database to annotate gene promoters identified from ChIP-seq results. Users can search the database based on gene id/symbol, or by specific tissue/cell type and filter result...
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MPSRCH
Uses the Smith-Waterman algorithm; runs at BLAST-like speeds without losing sensitivity.
website       summary

mreps
mreps is a tool for identifing tandemn repeats in DNA sequences.
website       summary

MRS
MRS is a biological data retrieval system that can be accessed over the web, or installed and used locally. MRS indexes several flat-file data sets for searching, including EMBL nucleotide, UniProt, PDB and KEGG. Searches can...
website       summary

mrsFAST-Ultra
mrsFAST-Ultra is designed to map short reads to reference genome assemblies; in a fast and memory-efficient manner.
website       summary

MSEA
Metabolite Set Enrichment Analysis (MSEA) performs enrichment analyses for (primarily human) metabolomic studies. It identifies patterns of metabolite concentration changes in a biologically meaningful context. MSEA uses a li...
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MuD
Mutation Detector (MuD) is a web server uses structural and sequence derived features to assess the impact of a given substitution on the protein function.
website       summary

Mulan
Mulan is a multiple sequence alignment tool. It employs novel algorithms such as TBA and multiTF to respectively perform alignments and discover transcription factor binding sites. Results can be viewed as dot-plots of indivi...
website       summary

MultiBind
Multiple Alignment of Protein Binding Sites (MultiBind) is a prediction tool for protein binding sites. Users input a set of protein-small molecule complexes and MultiBind predicts the common physio-chemical patterns responsi...
website       summary

Multifit
MultiFit is a web server for fitting multiple protein structures into their electron microscopy density map. The server takes as input a set of protein structures in the PDB format and an EM density map in the MRC format. The...
website       summary

Multi-Harmony
Multi-Harmony is an interactive web server for detecting sub-type specific sites in proteins starting from a multiple sequence alignment. Combines Sequence Harmony and Multi-Relief methods.
website       summary

MultiPhyl
MultiPhyl is a high-throughput Maximum Likelihood based phylogeny analysis program that allows researchers to create a virtual phylogenetic supercomputer from a group semi-idle desktop machines.
website       summary

Multi-Q
Multi-Q provides an automated data analysis tool for multiplexed protein quantitation based on iTRAQ labeling.
website       summary

Mutalyzer
Mutalyzer was primarily developed to check the description of sequence variants identified in a gene during genetic testing according to the rules of the standard human sequence variant nomenclature of the Human Genome Variat...
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MutDB
MutDB is a database that associates protein structural information with mutations and polymorphisms in gene sequences. The data is derived from dbSNP and Swiss-Prot, and can be browsed by gene name or searched by keyword or b...
website       summary

MutScreener
MutScreener is a human-specific primer design tool that considers gene annotation information to design primers for mutation screening. Users can provide custom gene annotation or use existing public gene annotations.
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MYBS
MYBS (Mining Yeast Binding Sites) is a tool for mapping Transcription factors (TFs) and their binding sites (TFBSs) that integrates both experimentally verified (ChIP-chip data) and predicted position weight matrixes (PWMs) f...
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myExperiment
myExperiment is an online research environment that supports the social sharing of bioinformatics workflows.
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MyHits
The MyHits server integrates several tools with a focus on protein annotation and the analysis of protein domains. Guest users have access to tools such as ClustalW and T-Coffee and databases like Swiss-Prot, Prosite and Inte...
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MySQL
MySQL is the world's most popular Open Source Database, designed for speed, power and precision.
website       summary

NAPS
NAPS is a web server for the prediction of specific residues involved in nucleic acid-binding proteins (NAPS) binding to nucleic acid. Amino acid residues involved in DNA and RNA binding are predicted.
website       summary

NAST
Nearest Alignment Space Termination (NAST) is a multiple sequence alignment server for comparative analysis of 16S rRNA gene sequences from bacteria and archaea.
website       summary

National Center for Biotechnology Information
NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information; est. 1988.
website       summary

Nature's Genome Gateway
A comprehensive web resource devoted to genomics. Sections include papers, news, the human-genome, and post-genomics.
website       summary

NBRP resources
The National BioResource Project (NBRP) is a system for collecting, preserving and providing bioresources for use as experimental materials for life science research. Thirty databases and an integrated database-retrieval syst...
website       summary

NCBI Assembly Archive
The NCBI Assembly Archive links publically available assembly information with the NCBI Trace Archive\'s raw sequence data.
website       summary

NCBI Bookshelf
Searchable collection of biomedical books linked to terms in PubMed abstracts; when viewing an abstract, click on Books link to see phrases in abstract hyperlinked to book sections.
website       summary

NCBI Clone Registry
A database that integrates information about genomic clones and libraries, including sequence data, genomic position, and distributor information.
website       summary

NCBI C++ toolkit
The NCBI C++ Toolkit is a collection of C++ modules developed by the NCBI for writing bioinformatics software and applications.
website       summary

NCBI Education
What is bioinformatics? Why use bioinformatics? excellent tutorials on BLAST and the Entrez search and retrieval system.
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NCBI Epigenomics
The Epigenomics database is a resource for whole-genome epigenetic data sets. Raw data is processed and mapped to genomic coordinates to generate 'tracks' that are a visual representation of the data. These data tracks can be...
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NCBI GEO
The Gene Expression Omnibus (GEO) database stores over 20,000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research commu...
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NCBI Human DNA Reference Sequence
Downloadable human DNA reference sequence as well as other reference genome sequences.
website       summary

NCBI Influenza Virus Sequence Annotation Tool
The NCBI Influenza Virus Sequence Annotation Tool is a web application for user-provided sequences. It can predict protein sequences encoded by an input flu sequence and produce a feature table that can be used for sequence s...
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NCBI Map Viewer
The NCBI Map Viewer provides graphical displays of features on NCBI\'s assembly of human genomic sequence data as well as cytogenetic, genetic, physical, and radiation hybrid maps.
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NCBI Resources
The National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site.
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NCBI Structure Group
Good starting point with links to databases and tools.
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NCBI Taxonomy Database
Taxonomic classification of all organisms with sequences in GenBank.
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ncFANs
The non-coding RNA Function ANotation server (ncFANs) is a web server for functional annotation of human and mouse long non-coding RNAs. Two strategies for lncRNA functional annotation are provided: 1) use of aspects of a cod...
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NCI Flicker
Flicker provides the means to compare images from different internet sources using a java-enabled web browser. It was originally designed for the comparison of 2D gels.
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NDB
NDB (Nucleic Acid Database) is a repository of three-dimensional structural information about nucleic acids.
website       summary

NDB Tools
The Nucleic Acid Database (NDB) Tools page includes RNAView and BPView, programs for the visualization and classification of RNA base pairs, motifs, and structures.
website       summary

NeAT
Network Analysis Tools (NeAT) is a suite of tools for the analysis of biological networks, clusters, classes and pathways. Tools are available as web services for integration into programmatic work flows.
website       summary

NEBcutter
NEBcutter finds non-overlapping open reading frames and sites for all enzymes that cut the sequence just once; max length is 100 kb.
website       summary

Negatome
The Negatome is a collection of protein and domain pairs that are unlikely to be engaged in direct physical interactions. The database currently contains experimentally supported non-interacting protein pairs derived from two...
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NEP
NEP (Neutralization-based Epitope Prediction) is a web server for antibody-specific epitope prediction based on antibody neutralization of viral strains.
website       summary

NetCSSP
A web application based on contact-dependent secondary structure propensity calculations for predicting chameleon sub-sequences that may contribute to amyloid fibril formation. NetCSSP also contains precalculated non-native s...
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Netgene2
The NetGene2 server is a service producing neural network predictions of splice sites in human, C. elegans and A. thaliana DNA.
website       summary

NetMHC-3.0
NetNHC-3.0 is a web server for the prediction of human, mouse or monkey MHC Class I-peptide binding. Predictions are made for peptides of 8-11 amino acid length using artificial neural networks and weight matrices.
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NetOGlyc Prediction Server
Predicts mucin type GalNAc O-glycosylation sites in mammalian proteins.
website       summary

NetPhhosK
The NetPhosK web-server produces neural network predictions of kinase specific eukaryotic protein phosphoylation sites.
website       summary

NetPhos
NetPhos is a neural network-based method for predicting potential phosphorylation sites at serine, threonine or tyrosine residues in protein sequences
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NetVenn
NetVenn is a network-based web platform for the comparison and analysis of gene lists by combining Venn diagram and gene set enrichment.
website       summary

NetworkAnalys
NetworkAnalyst is designed to perform protein-protein interacton (PPI) network analysis from gene expression data. It integrates differential expression analysis, network construction and network analysis.
website       summary

Network of Cancer Genes
The Network of Cancer Genes (NCG) collects and integrates data on 736 human genes that are mutated in various types of cancer. For each gene, NCG provides information on duplicability, orthology, evolutionary appearance and t...
website       summary

NeuroPID
NeuroPID is a prediction tool for neuropeptide precursors (NPPs) and neuromodulators.
website       summary

Neuropred
NeuroPred is a tool designed to predict cleavage sites at basic amino acid locations in neuropeptide precursor sequences. Neuropred also computes the mass of the predicted peptides with or without selected post-translational ...
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Neuroscience Information Framework
A dynamic inventory of Web-based neuroscience resources: data, materials, and tools accessible via any computer connected to the Internet. An initiative of the NIH Blueprint for Neuroscience Research, the Neuroscience Informa...
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NEWT
NEWT is the taxonomy database maintained by the UniProt group.
website       summary

NGSmethDB
NGSmethDB contains methylation data derived from next-generation sequencing (NGS). Two cytosine methylation contexts (CpG and CAG/CTG) are considered. Through a browser interface, the user can search for methylation states in...
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NHGRI Micorarray Project
Protocols, analysis and resources; BLAST against the 15K set cDNA library clones (from 15,000 human UniGene clusters; clones are available).
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NHGRI Policy and Ethics
Critical issues and legislation surrounding genetic research. Hosted by the National Human Genome Resarch Institute (NHGRI).
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NIASGBdb
The National Institute of Agrobiological Sciences Genebank Project database (NIASGBdb) consists of a genetic resource database and a plant diseases database, linked by a web retrieval database. The genetic resources database ...
website       summary

NJplot
NJplot is a tool for visualizing binary trees such as the phylogenetic trees output from the PHYLIP programs. Available for several platforms including Windows, MacOS, Linux and Solaris.
website       summary

NLProt
NLProt is a tool for finding protein names in natural language text. This data-mining method is a useful approach for extracting protein UniprotIDs from research articles for the construction of custom datasets and/or databas...
website       summary

NMR Constraints Analyser
NMR Constraints Analyser is a web tool that provides an automatic graphical analysis of the NMR experimental constraints atom by atom.
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NNcon
Using 2D-recursive neural networks, NNcon is a web server for predicting protein contact maps.
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NNDB
The Nearest Neighbor Database (NNDB) is a web-based resource for disseminating parameter sets for predicting nucleic acid secondary structure stabilities. For each set of parameters, the database includes the set of rules wit...
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NOBAI
NOBAI web server facilitates the search for the evolutionary history embedded in the structure of functional RNA molecules.
website       summary

NOMAD-Ref
Normal Mode Analysis, Deformation, and Refinement (NOMAD-Ref) provides tools for calculating functionally relevant movements in biological macromolecules. This resource provides tools for investigating different conformations...
website       summary

Non-B DB
Non-B DB is a non-canonical (non-B) structure database database integrating annotations and analysis of non-B DNA-forming sequence motifs. The database provides alternative DNA structure predictions, including Z-DNA motifs, q...
website       summary

Non-Coding RNA database
Non-translatable RNA transcripts that appear to work at the RNA level.
website       summary

NORSp
NORSp (predictor of NOn-Regular Secondary Structure) is a tool for predicting disordered regions in proteins.
website       summary

NQ-Flipper
NQ-Flipper recognizes unfavorable rotamers of Asn and Gln residues in protein structures.
website       summary

NRPS-PKS
NRPS-PKS is an tool comprising four integrated databases for the analysis of large multi-enzymatic multi-domain megasynthases. The user can submit a query sequence to search for domains or view the properties of the products.
website       summary

NRPSpredictor2
NRPSpredictor2 is a web server for predicting bacterial non-ribosomal peptide synthetases (NRPS) adenylation domain specificity.
website       summary

NRSAS
Nuclear Receptor Structure Analysis Server (NRSAS) is a multi-purpose collection of tools for the analyses of nuclear hormone receptors.
website       summary

nsSNPAnalyzer
nsSNPAnalyzer is a tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) is phenotypically neutral or disease associated.
website       summary

NTMG
NTMG (N-Terminal Truncated Mutants Generator) is a tool for generating multiplex PCR primers for designing N-terminal truncated mutants.
website       summary

Nucleic Acids Research Database Issue
Molecular Biology Database Collection with links to databases with short descriptions of each.
website       summary

NXSensor
Nucleosome eXclusion Sensor (NXSensor) finds potential nucleosome-free regions of DNA sequences. NXSensor can be used to assess the likelihood of nucleosome formation in regions involved in gene regulation and other aspects o...
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ODB
ODB (Operon DataBase) contains all known and conserved operons in completely sequenced genomes.
website       summary

oGNM
Online Guassian Network Model (oGNM) calculates the equilibrium dynamics of any structure submitted in PDB format, using the Gaussian Network Model (GNM), a network model for representing biomolecules.
website       summary

OligoArray
OligoArray is free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction. A database of pre-designed oligonucleotide microarray probes for organisms with a fully sequen...
website       summary

OligoCalc
OligoCalc calculates the physical properties of single- and double-stranded DNA and RNA molecules including melting temperature (multiple methods), concentration, molecular weight, and absorbance at 260 nanometers. OligoCalc ...
website       summary

OligoHeatMap
OligoHeatMap is an online tool for estimation of melting temperatures for sets of oligonucleotides and positioning of oligomers within sets of aligned sequences. Oligomer positioning on sequences is displayed graphically.
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OligoWalk
OligoWalk is an online sever for designing efficient siRNA targeting a given mRNA sequence. By calculating thermodynamic features of sense-antisense hybidization, OligoWalk predicts the free energy changes of oligonucleotides...
website       summary

OligoWiz
OligoWiz 2.0 is a client for microarray probe design that allows for the integration of sequence annotations, probe quality parameters, and the placement of multiple probes per transcript.
website       summary

OMA
OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes.
website       summary

OmicBrowse
OmicBrowse is a genome browser designed as a scalable system for maintaining numerous genome annotation datasets. Multiple users may access a common dataset.
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OMIM
Online Mendelian Inheritance in Man; catalog of human genes and genetic disorders with descriptive text, references, and links to many NCBI resources including GenBank and PubMed.
website       summary

OMPdb
OMPdb is a database of integral beta-barrel outer membrane proteins from Gram-negative bacteria, classified in functional families. OMPdb entries contain cross-references to other databases, references to the literature and a...
website       summary

OncoSearch
OncoSearch is a cancer gene search engine with literature evidence.
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One-Block CYRCA
One-Block CYRCA is a program for identifying blocks (local ungapped profiles of the most conserved regions of protein families and domains) in a multiple sequence alignment based on the LAMA and CYRCA block-to-block alignment...
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ONJava.com
O'Reilly Network's source for Java news and information.
website       summary

Ontology Lookup Service
The Ontology Lookup Service provides interactive and programmatic interfaces to query and browse a suite of biomedical ontologies and controlled vocabularies. Users can also navigate the relationships between terms and obtain...
website       summary

Onto-Tools
Onto-Tools is a suite of tools for data mining based on information from Gene Ontology (GO). Onto-Tools includes an annotation database and the data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-...
website       summary

OPAAS
Optimal, Permuted, and Other Alternative Alignments of Protein Structures (OPAAS) is a tool for investigating structural neighbors that can calculate a structural alignment for two protein structures.
website       summary

Opal Web Services for Biomedical Applications
Opal Web Services for Biomedical Applications is a production web server. Powered by Opal, it allows users to use scientific applications easily as web services without any modification to the scientific codes.
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Open Bioinformatics Foundation
The Open Bioinformatics Foundation is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics.
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OpenHelix
Repository of bioinformatic tutorials and resources. Some are open access, others have restricted access.
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OpenHUSAR
Open HUSAR (Heidelberg Unix Sequence Analysis Resources) contains suite of bioinformatics pipelines including tasks oriented to protein annotation by homology (ProtSweep), by domain analysis (DomainSweep), and by secondary st...
website       summary

oPOSSUM
oPOSSUM is a web-based system for the detection of over-represented transcription factor binding sites in the promoters of sets of genes.
website       summary

OPTIMIZER
OPTIMIZER is an application that optimizes the codon usage of a DNA sequence. This server can be used to predict and optimize the level expression of a gene in heterologous gene expression systems.
website       summary

OptiTope
OpiTope identifies the optimal set of peptides or epitopes for a vaccine given constraints such as MHC allele probabilities, peptide mutation rates and maximum number of selected peptides. Incorporated as part of the EpiToolK...
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ORegAnno
The Open REGulatory ANNOtation database (ORegAnno) is a collection of literature-curated regulatory regions, transcription factor binding sites (TFBS) and regulatory mutations.
website       summary

OREST
Online Resource for EST (OREST) analysis is a EST analysis pipeline which allows rapid analysis of large amounts of ESTs or cDNAs from mammals and fungi. Functional annotation of the dataset is also included via either FunCat...
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ORF Finder
Finds all open reading frames in a sequence.
website       summary

Orphelia
Orphelia is a machine learning program for predicting genes in short DNA sequences from metagenomic sequencing projects. The program encompasses fragment length specific prediction models for chain termination sequencing and ...
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OrthoDB
OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes across 44 vertebrates, 25 arthropods, and 46 fungi. OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. The database...
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Orthologue Search Service
BLAST a protein sequence then perform automated phylogenetic analysis to detect orthologous sequences.
website       summary

OrthoSelect
OrthoSelect web server detects orthologous gene sequences in EST libraries and outputs orthologous gene alignments. Annotations, data matrices for each gene, and the gene alignments may also be visualized.
website       summary

OSCAR
OSCAR (Open System for Clustering Analysis) is a platform for cluster analysis of microarray data.
website       summary

The Osprey Network Visualization System
Application for graphically representing physical and genetic biological interactions; is coupled with the General Repository of Interaction Datasets (The GRID); available for Unix and Windows.
website       summary

OSU Bioinformatics and Computational Biology
The website of the Ohio State University Human Cancer Genetics Bioinformatics group. This site has many resources, including databases of promoters and transcription factors, software tools to predict potential P53 consensus ...
website       summary

P2CS
P2CS is a database for prokaryotic two-component systems (TCSs). The database annotates and classifies TCS proteins from completely sequenced prokaryotic genomes and metagenomes. TCS complements can be browsed by metagenome, ...
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PAComplex
PAComplex is a web server for inferring peptide antigen families and binding models from T-cell receptor-peptide MHC complexes.
website       summary

PAIR
The predicted Arabidopsis interactome resource (PAIR) contains experimentally reported molecular interactions and predicted interactions in Arabidopsis thaliana. PAIR predicts interactions by a fine-tuned support vector machi...
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PAL2NAL
PAL2NAL converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. Synonymous (Ks) and non-synonymous (Ka) substitution rates can be calculated.
website       summary

PaLS
Pathway and Literature Strainer (PaLS) highlights those members on a user inputted list that share descriptors from PubMed, GO, KEGG and Reactome.
website       summary

Pancreatic Expression database
The Pancreatic Expression database (PED) is a repository for pancreatic-derived -omics data. It includes easurements derived from transcriptomics, proteomics, genomics and miRNA profiles from various pancreas-centred reports ...
website       summary

PANDORA
The PANDORA web server integrates annotations for the biological analysis of sets of genes, proteins or peptides.
website       summary

PANTHER
Protein Analysis THrough Evolutionary Relationships (PANTHER) is a comprehensive software system for inferring the functions of genes based on their evolutionary relationships. Phylogenetic trees of gene families form the bas...
website       summary

PANTHER Tools
The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relation...
website       summary

PAP
Promoter Analysis Pipeline (PAP) can identify potential transcriptional regulators for sets of co-expressed genes and identify potential regulatory targets of transcription factors.
website       summary

ParAlign
ParAlign provides a service for sequence similarity searching powered by parallel computing technology. The two comparison algorithms used are Smith-Waterman and ParAlign (a heuristic method for sequence alignment).
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ParameciumDB
ParameciumDB is a database built with the GMOD toolkit to integrate the genome and biology of the ciliate Paramecium tetraurelia. Post-genomic data from proteome and transcriptome studies has been incorporated along with pred...
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Parasite-Genome
Parasite genome databases and genome research resources.
website       summary

PARSESNP
Project Aligned Related Sequences and Evaluate SNPs (PARSESNP) is a tool for the analysis of polymorphisms in genes.
website       summary

ParticleStats
ParticleStats is a web server for particle motility analysis such as cytoskeleton. Input is X,Y coordinates of objects in time and output is novel analyses, graphical plots and statistics for motile objects.
website       summary

PartiGeneDB
PartiGeneDB is a database of about 300 partial genomes from eukaryotic organisms that have been assembled from EST data.
website       summary

PAST
Polypeptide Angles Suffix Tree (PAST) provides methods for searching three-dimensional protein structures and identifying frequent common substructures (structural motifs) using an approach independent of the sequence of amin...
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PASTA 2.0
PASTA 2.0 is an improved server for protein aggregation prediction.
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PA-SUB
PA-SUB (Proteome Analyst Specialized Subcellular Localization Server) can be used to predict the subcellular localization of proteins using established machine learning techniques.
website       summary

PatchDock
PatchDock is an algorithm for molecular docking. The input is two molecules of any type: proteins, DNA, peptides, drugs. The output is a list of potential complexes sorted by shape complementarity criteria.
website       summary

PathBLAST
PathBLAST is a tool for cross-species comparison of protein interaction networks. PathBLAST takes a short protein interaction path as input and searches against an available protein-protein interation network specified by the...
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Pathema
Pathema is a site for understanding, detecting, diagnosing and treating an established set of six target NIAID Category A-C pathogens: Category A priority pathogens; Bacillus anthracis and Clostridium botulinum, and Category ...
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PathExpress
PathExpress is a tool developed to interpret gene expression data obtained from microarray experiments by identifying and visualizing the most relevant metabolic pathways associated with a subset of genes (e.g. differentially...
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PathGuide
The PathGuide - Pathway Resource List (PRL) is a database of 250+ links to resources for protein-protein interactions, metabolic and signalling pathways, transcription factor and genetic interaction networks, pathway diagrams...
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PathPred
PathPred is an enzyme catalyzed metabolic pathway prediction server. Beginning with a query compound and chemical logic of enzymatic reactions (chemical structure transformation patterns of small molecules), biodegradation pa...
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Pathway Commons
Pathway Commons is a collection of publicly available pathway data from multiple organisms. Pathway Commons provides a web-based interface that enables biologists to browse and search a comprehensive collection of pathways fr...
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Pathway Explorer
Pathway Explorer is a tool for visualizing high throughput expression data simultaneously with biological pathway data available from KEGG, BioCarta, and GenMAPP.
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Pathway extraction
The pathway extraction tool is a part of the network analysis tool suite (NeAT). Given a metabolic network, the tool extracts a subnetwork that connects a list of input compounds, reactions, EC numbers or enzyme-coding genes....
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Pathway Hunter Tool
Pathway Hunter Tool (PHT) uses shortest path analysis to reconstruct and visualize biochemical pathways. The user can find the shortest path between two metabolites, or find all reachable products or educts for a given metabo...
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Pathway Miner
Pathway Miner is a tool for searching lists of genes for associations in known pathway data from KEGG, BioCarta, and GenMAPP. Also provides statistical analyses.
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PatMatch
PatMatch is a pattern matching tool that allows you to search for short (<20 residues) nucleotide or peptide sequences and can accomodate ambiguous/degenerate patterns.
website       summary

Patrocles
The Patrocles database compiles DNA sequence polymorphisms (DSPs) that are predicted to perturb miRNA-mediated gene regulation.
website       summary

PAZAR
PAZAR is an open access and open source database of transcription factor and regulatory sequence annotation with associated web interface and programming tools designed to submit and query data related to the regulation of ge...
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PBE
Protein Blocks Expert (PBE) uses a structural alphabet of short structural motifs to compare protein structures. PBE uses as its structural alphabet a set of protein blocks derived from structurally aligned homologous protein...
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PBEQ-Solver
PBEQ-Solver is a wb based graphical user interface to read biomolecular structures, solve the Poisson-Boltzmann equations and interactively display the eletrostatic potential.
website       summary

PBIL
Pole Bio-Informatique Lyonnais (PBIL) provides access to sequence databanks (EMBL, GenBank, SWISS-PROT, PIR) and to many tools of nucleic acid and protein sequence analyses.
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PCDB
PCDB is a database of protein conformational diversity. For each protein, the database contains the redundant compilation of all the corresponding crystallographic structures obtained under different conditions. These structu...
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PCDDB
The Protein Circular Dichroism Data Bank (PCDDB) is a public repository for circular dichroism (CD) and synchrotron radiation CD (SRCD) spectral data and their associated experimental metadata. All entries undergo validation ...
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PCE
PCE (Protein Continuum Electrostatics) is an interface to electrostatic potentials and pKa calculations using the MEAD package.
website       summary

PCFamily
The PCFamily server identifies template-based homologous protein complexes or families, and infers functional modules for query proteins. Useful for binding model visualizations and annotating query proteins.
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Pcleavage
Pcleavage is a tool that uses a support vector machine to predict immunoproteasome and constitutive proteasome cleavage sites in antigenic sequences.
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Pcons.net
Pcons.net is a protein structure prediction meta server that provides automated tools for protein structure prediction and analysis using a consensus approach.
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PCRPi-DB
Presaging Critical Residues in Protein Interfaces Database (PCRPi-DB) is a public repository that archives computationally annotated hot spots in protein complexes for which the 3D structure is known. Hot spots have been anno...
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PCRTiler
PCRTiler web server tool allows for the automated design of tiled primer pairs for any number of genomic loci. Based on Primer3 and BLAST analysis for cross-hybridization.
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PDA
PDA (Pipeline Diversity Analysis) is a server which searches for polymorphic sequences in large databases, and estimates their genetic diversity. Results contain sequence alignments (generated by ClustalW) and include statist...
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PDA
Primer Design Assistant (PDA) is a PCR primer design tool that will accept batch submissions of query sequences.
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PDB2PQR Server
Server that allows users to convert PDB files into PQR files by adding missing atoms, optimizing hydrogen bonding and assigning atomic charge and radius parameters. The resulting PQR file can be used for electrostatic calcula...
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PDBe
The Protein Data Bank in Europe (PDBe) manages the international archive of biomacromolecular structure data as one of the partners in the Worldwide Protein Data Bank. PDBe has developed a browser to access and analyze the st...
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PDBe (formerly MSD)
The Protein Data Bank in Europe (PDBe) is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures. The database infrastructure is based on the remediated PDB ar...
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pdbFun
pdbFun allows the user to search the PDB as a database of annotated residues. One can limit the search by annotations such as domains, binding sites, active sites, solvent exposure and residue type.
website       summary

PDB_Hydro
PDB_Hydro provides tools for mutating and solvating structures of biological macromolecules like proteins or DNA. It identifies strongly and poorly solvated exposed surfaces of structures in an effort to help identify potenti...
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PDB Related Databases
PDB Related Datbases present a series of databases that run parallel to the PDB. DSSP holds the secondary structure of the proteins. PDBREPORT holds reports on the structure quality and lists errors. HSSP holds a multiple seq...
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PDBselect
PDBselect is a list of representative protein chains with low mutual sequence identity selected from the protein data bank (PDB) to enable unbiased statistics. PDBfilter-select is an online service to generate user-defined se...
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PDBSiteScan
PDBSiteScan takes a PDB file as input, and searches for stuctural matches with the PDBSite set of known functional sites.
website       summary

pDRAW32
pDRAW32 is a multi-function tool with features including: graphical displays useful for drawing plasmids, sequence analysis and editing, virtual agarose gel plots and homology plots.
website       summary

PEACE
Parallel Environment for Assembly and Clustering of Gene Expression (PEACE) web tool performs high-throughput ab initio clustering of transcript fragment sequences from next-generation sequencing platforms.
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PEDRo
Software and schemata for modelling, capturing and disseminating proteomics experimental data
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Pegasys: workflow management for bioinformatics
Pegasys is a a flexible, modular and customizable software system that coordinates the execution of multiple biological sequence analysis tools and facilitates the integration of their output. The software allows users to cre...
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PEP-SiteFinder
PEP-SiteFinder is a web server tool for the blind identification of peptide binding sites on protein surfaces.
website       summary

PepBuild
PepBuild is a tool that facilitates the construction, from known sequence and secondary/tertiary structures, of capped or uncapped proteins. The output generated is in PDB format.
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PEP-FOLD
PEP-FOLD uses a hidden Markov model-derived structural alphabet for de novo modeling of 3D conformations of peptides between 9-25 amino acids in aqueous solution. Updates to PEP-FOLD allow for modeling of linear and disulphid...
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pepMMsMIMIC
pepMMsMIMIC is a peptidomimetic compound virtual screening tool based on a multi-confromers 3D-similarity search strategy. Using as input the 3D structure of a peptide bound to a protein, pepMMsMIMIC suggests which chemical s...
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PepServe
PepServe is a web server for peptide analysis, clustering and visualization.
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PeptideMass
Cleaves a protein sequence with a chosen enzyme and computes masses of the generated peptides.
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PEPVAC
PEPVAC is a tool to assist in the development of multi-epitope vaccines. It is optimized for this task by predicting peptides with the ability to bind to several human leukocyte antigens that have similar peptide binding spec...
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PepX
PepX is an exhaustive data set of all protein-peptide complexes available in the Protein Data Bank with peptide lengths up to 35 residues. Complexes have been clustered based on their binding interfaces rather than sequence h...
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Perl.com
The homepage of the perl programming language.
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Perl Mongers
Perl Mongers - The Perl advocacy people.
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Perl Monks
Perl community site
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PeroxisomeDB
PeroxisomeDB contains the complete peroxisomal proteome of Homo sapiens and Saccharomyces cerevisiae, as well as 35 newly sequenced eukaryotic genomes including fungi, yeasts, plants and lower eukaryotes. PeroxisomeDB 2.0 int...
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Personal Genome Browser
The Personal Genome Browser allows on to visualize functions of genetic variants.
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PETfold & PETcofold
The PETfold and PETcofold web servers for the analysis of multiple RNA sequences for common RNA structure and for RNA-RNA interaction sites. Analysis is based on probablistic evolutionary an thermodynamic models.
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Pfam
Pfam is a database of protein families and domains. The database uses HMMER3, the latest version of the popular profile hidden Markov model package. Pfam release 24.0 contains 11,912 families.
website       summary

Pfold
The Pfold server takes an alignment of RNA sequences as input and predicts a common secondary structure.
website       summary

PFP
PFP (Patch Finder Plus) is a tool for extracting and displaying positive electrostatic patches on protein surfaces which can be indicative of nucleic acid binding interfaces.
website       summary

PharmaGist
PharmaGist is a web server for detecting pharmacophores or the spatial arrangement of features that enables a molecule to interact with a specific target receptor. Users input a set of structures of molecules that bind with t...
website       summary

PharmMapper
PharmMapper is a web server that identifies potential drug targets from its PharmTargetDB for a given input molecule. Potential targets are identified from a prediction of the spatial arrangement of features essential for a g...
website       summary

PHAST
PHAST (PHAge Search Tool) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. PHAST also generates downloadable, high quality,...
website       summary

PHEMTO
Protein pH-dependent Electric Moment Tools (PHEMTO) is a web server for evaluating protein electrostatic characteristics relative to their molecular interactions. Input is the atomic coordinate file in PDB format; output is e...
website       summary

PhenoHM
PhenoHM is a human-mouse comparative phenome-genome server that facilitates cross species identification of genes associated with orthologous phenotypes.
website       summary

PhenomicDB
PhenomicDB integrates the genotype and phenotype information of several organisms from public data sources. The mapping of phenotypic data fields allows cross-species phenotype comparison.
website       summary

PHEPS
pH-dependent Protein Electrostatics Server (PHEPS) performs global and local pH-dependent electrostatic analysis of protein structures. The user can supply a PDB ID or upload a coordinate file.
website       summary

PhEVER
The PhEVER database provides accurate evolutionary and phylogenetic information to analyse the nature of virus-virus and virus-host lateral gene transfers. It is a database of homologous families both (i) between sequences fr...
website       summary

PHIRE
Phage In silico Regulatory Elements (PHIRE) is a standalone program in Visual Basic which performs a string-based search on bacteriophage genome sequences discovering and extracting blocks displaying sequence similarity corre...
website       summary

phiSITE
phiSITE is a database of gene regulation in bacteriophages. It collects experimentally confirmed or predicted regulatory elements (promoters, operators, terminators and attachment sites) from bacteriophages belonging to Sipho...
website       summary

Phobius
Phobius is a combined transmembrane topology and signal peptide predictor. The server also allows for constrained and homology-enriched predictions.
website       summary

PHOG
The PHOG web server identifies orthologs based on precomputed phylogenetic trees in the PhyloFacts resource. Users may target different taxonomic distances and precision levels by using tree-distance thresholds.
website       summary

Phosfinder
Phosfinder uses a structural comparison algorithm to identify phosphate binding sites in protein structures. It scans a query structure in PDB format against a set of known 3D phosphate binding motifs and outputs a visual dis...
website       summary

PHOSIDA 2011
PHOSIDA database manages posttranslational modification sites of various species ranging from bacteria to human. It contains phosphorylated, N-glycosylated or acetylated sites. All sites are obtained from high-resolution mass...
website       summary

PhosPhAt
The Arabidopsis Protein Phosphorylation Site Database (PhosPhAt 3.0) contains information on Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments by different research groups...
website       summary

Phospho3D 2.0
Phospho3D is a database of 3D structures of phosphorylation sites derived from Phospho.ELM. The database provides the results of a large-scale structural comparison of the 3D zones versus a representative dataset of structure...
website       summary

Phospho.ELM
Database of experimentally verified phosphorylation sites in eukaryotic proteins. Annotations are done manually and database entries come from and are linked back to scientific literature. Phospho.ELM incorporates the data fo...
website       summary

Phospho.ELM
The Phospho.ELM resource is a relational database designed to store in vivo and in vitro phosphorylation data extracted from the scientific literature and phosphoproteomic analyses. The resource comprises serine, threonine an...
website       summary

PhosphoSite
PhosphoSite is a curated database of in vivo human and mouse phosphorylation sites. The database contains peptide sequences and locations within domains and motifs for the phosphorylation sites, and links to useful resources ...
website       summary

Phred/Phrap/Consed System
UNIX-based, base-calling, sequence assembly and finishing tools used by most genome sequence centres; free for non-commercial use.
website       summary

PHUSER
Primer Help for Uracil Specific Exision Reagent (PHUSER) is a tool for designing primers specifically for USER fusion and USER cloning applications. Standard primer analyses are also conducted.
website       summary

Phydbac2
Phydbac2 (Phylogenomic display of bacterial genes) is a tool to visualize and explore the phylogenomic profiles of bacterial protein sequences. It also allows the user to view sequence similarity across different organisms, a...
website       summary

PhyleasProg
PhyleasProg is a web server for evolutionary analyses. Users input a list of Ensembl protein IDs and a list of species as inputs.
website       summary

Phylemon
Phylemon is a server that integrates a suite of tools for multiple sequence alignment, phylogeny, and evolutionary tests from the most popular stand-alone phylogenetic and evolutionary analysis programs. Phylemon 2.0 has an i...
website       summary

PHYLIP
Comprehensive set of programs for phylogenetic analyses; available for PC and Mac; source code available for easy compiling in UNIX.
website       summary

PhyloDome
PhyloDome is a tool with which you can visualize and analyze the phylogenetic distribution of one or more eukaryotic domains.
website       summary

Phylogeny.fr
Phylogeny.fr is a seamless automation of the various components in pylogenetic analyses from identification of homologous sequences, construction of multiple alignments, phylogenetic reconstruction to graphical representation...
website       summary

PhylomeDB v3.0
PhylomeDB is a public database for genome-wide collections of gene phylogenies (phylomes). It is also a major source for phylogeny-based orthology and paralogy predictions. For each protein-coding gene in a seed genome, the d...
website       summary

PhyloPars
The PhyloPars web server allows for easy, efficient estimation of metabolic parameters as inferred from observations on species that are phylogenetically related.
website       summary

PhyloPat
PhyloPat is a webserver which can be used to query the orthologies of all complete genomes within the EnsMart database using phylogenetic patterns. This enables the determination of sets of genes that occur only in certain ev...
website       summary

Phyloscan
Phyloscan is a web server that locates transcription regulating binding sites by exploiting binding site evolutionary conservation and repeats in promoter regions. Mixed aligned and unaligned sequence data may be used.
website       summary

PI2PE
PI2PE (Protein Interface/Interior Prediction Engine) consists of three predictors (WESA, cons-PPISP, and DISPLAR) for predicting solvent accessibility and interface residues from the structure of a protein-binding or DNA-bind...
website       summary

PIC
Protein Interactions Calculator (PIC) is a server which recognizes various kinds of interactions; such as disulphide bonds, hydrophobic interactions, hydrogen bonds, aromatic interactions, and ionic interactions within a prot...
website       summary

PicXAA-Web
PicXAA-Web is a web tool for probablistic alignment of multiple biological sequences using probabilistic non-progressive alignment algorithms. Multiple protein, DNA and RNA sequences may be analyzed.
website       summary

PIE
The Protein Interaction information Extraction system (PIE) is a configurable web server for extraction of protein-protein interactions from literature. Both co-occurrence of proteins in text and predefined phrase patterns fo...
website       summary

PileLineGUI
PileLineGUI is a desktop environment for manipulating, browsing and analyzing genome position files from next generation sequencing experiments, with specific support of somatic mutation finding studies. A genome browser tool...
website       summary

PILGRM
The Platform for Interactive Learning by Genomics Results Mining (PILGRIM) is an interactive data driven discovery platform for biology. Expression levels of known relevant genes (specified by the user) are used to discover a...
website       summary

PINT
Pathway INtegration Tool (PINT) allows integration and annotation of systems biology markup language (SBML) files from a variety of sources. Gene list files are also accepted.
website       summary

PINTA
PINTA is a web tool for the prioritization of candidate genes based on the differential expression of their neighborhood in a genome-wide protein-protein interaction network. PINTA is available for 5 species (human, mouse, ra...
website       summary

PINTS
Patterns in Non-homologous Tertiary Structures (PINTS) finds similarities between protein structures containing structural patterns and provides a statistical measure of local structural similiarities.
website       summary

PipeAlign
PipeAlign takes one or more protein sequences as input and analyzes them in a five-step process during which searches for sequence homologues, analyses of multiple sequence alignments, and hierarchical relationships between p...
website       summary

PipMaker
PipMaker computes alignments of similar regions in two DNA sequences. MultiPipMaker allows the user to see relationships among more than two sequences.
website       summary

PIQMIe
PIQMIe (Proteomics Identifications & Quantitations Data Management & Integration Service) is a web server for semi-quantitative proteomics data management and analysis.
website       summary

PiRaNhA
The PiRaNhA web server predicts the location of RNA binding residues in protein sequences using a support vector machine. Up to 10 protein sequences may be submitted.
website       summary

PIR - Protein Information Resource
PIR is an integrated bioinformatics resource. The Protein Sequence Database (PSD), a functionally annotated database of protein sequences, is located at PIR.
website       summary

PISCES
PISCES (Protein Sequence Culling Server) allows the user to weed out sequences from a set in order to obtain a subset of relatively high PDB structure quality and/or mutual sequence identity.
website       summary

pknotsRG
pknotsRG is a server for single sequence RNA secondary structure prediction including pseudoknots; source code, binary executable, and web service available.
website       summary

pKNOT-v2
pKNOT (Protein Knot) is a tool that can detect knots in proteins as well as providing information on knotted proteins in PDB. pKNOT-v2 has been updated with a homology modeling tool such that the server can now accept protein...
website       summary

PLAN2L
A web based tool that integrates text mining and information extraction techniques to access useful information for analyzing genetic, cellular and molecular aspects of Arabidposis thaliana.
website       summary

PLANdbAffy
PLANdbAffy contains the results of the alignment of probe sequences from five Affymetrix expression microarrays to the human genome. Probes matching the transcript-coding regions in the correct orientation have been determine...
website       summary

Plant MicroRNA Database
The plant miRNA database (PMRD) integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary stru...
website       summary

Plant Resistance Genes database
PRGdb is a database provides a comprehensive overview of resistance genes (R-genes) in plants. PRGdb holds more than 16,000 known and putative R-genes belonging to 192 plant species challenged by 115 different pathogens and l...
website       summary

PlantTFDB
Plant Transcription Factor Database (PlantTFDB) is database that attempts to identify a comprehensive set of plant genes coding for transcription factors. A web interface to the database allows users to browse by species, sea...
website       summary

PlantTFDB 2.0
The PlantTFDB 2.0 plant transcription factor (TF) database contains detailed annotation including general information, domain feature, gene ontology, expression pattern and ortholog groups, as well as cross references to vari...
website       summary

PlasMapper
Web server that automatically generates and annotates circular plasmid maps. The tool has: a built in set of features that can be displayed (ie. RE sites, tags, ORFs, etc.); allows users to define custom features to display; ...
website       summary

PLAST-ncRNA
PLAST-ncRNA is an online tool for aligning distantly similar non-coding RNA sequences to a genome using the Probalign program. Useful for detection of potential homologous ncRNA sequences in large genomes.
website       summary

PLecDom
PLecDom is a program for the detection of Plant Lectin Domains in a polypeptide or EST sequence. In the web server, users evaluate their input sequence for lectin domains, classify the identified domains into substrate classe...
website       summary

PlnTFDB
Plant Transcription Factor Database (PlantTFDB) is database that attempts to identify a comprehensive set of plant genes coding for transcription factors. A web interface to the database allows users to browse by species, sea...
website       summary

PlnTFDB
The Plant Transcription Factor Database (PlnTFDB) is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species whose genomes have...
website       summary

PlotRep
PlotRep is a tool for the visual analysis of dispersed genomic repeats. The tool is designed to merge fragments belonging to the same copy of a repeat and allows for the inspection of the results using a dot-plot like graphic...
website       summary

PMG
The Protein Movie Generator (PMG) is a tool to generate protein pictures, animations, and movies.
website       summary

PmiRKB
Plant miRNA knowledge base (PmiRKB) provides four major functional modules. In the 'SNP' module, single nucleotide polymorphism (SNP) data of seven Arabidopsis (Arabidopsis thaliana) accessions and 21 rice (Oryza sativa) subs...
website       summary

POBO
POBO is a tool to summarize, verify and screen predetermined cis-element motifs from a set of sequences. POBO reports the results in as understandable format as possible for biologists.
website       summary

pocketZebra
pocketZebra is a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families.
website       summary

POCO
POCO searches a set of promoters from co-expressed genes for nucleotide patterns that are over-represented.
website       summary

PolyBayes
UNIX-based SNP discovery from redundant sequences; integrated with Phred/Phrap/Consed infrastructure (see DNA -- Contig Assembly); free for non-commercial use.
website       summary

PolyPhen
Polymorphism Phenotyping (PolyPhen) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein.
website       summary

PolyPhred
UNIX-based tool for sequence trace based genotyping; integrated with Phred/Phrap/Consed (see DNA -- Contig Assembly); free for non-commercial use.
website       summary

PolyQ
PolyQ database is a collection of sequences of all human proteins containing runs of seven or more glutamine residues and their annotated sequences with domain information. PolyQ can be interrogated such that the sequence con...
website       summary

PolySearch
PolySearch allows users to conduct comprehensive and associative queries, such as given X, find all Y's, where X or Y can be diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolite...
website       summary

POLYVIEW-MM
POLYVIEW-MM is a web server that integrates high quality animation of molecular motion into structural and functional analysis of macromolecules. Structural annotations such as mapping of known interaction sites from structur...
website       summary

Pomelo II
Pomelo II is a web-server for the analysis of gene (and protein) expression and tissue array data. Different statistical tests are applied depending on the input data. Links are also provided to additional sources of informat...
website       summary

PONGO
PONGO allows users to compare topology predictions of membrane proteins made by four different predictors (MEMSAT, TMHMM, ENSEMBLE, and PRODIV). It also displays a signal peptide prediction determined with SPEP.
website       summary

POPS
Parameter OPtimised Surfaces (POPS) is an algorithm to calculate accessible surfaces areas at atomic and residue level.
website       summary

POPSCOMP
POPSCOMP is a system for analysing the interaction between components of complexes based on calculations of the accessible surface that is buried when the complex is formed.
website       summary

POSA
POSA (Partial Order Structure Alignment) is a web server for multiple protein structure alignment.
website       summary

PosMed
To assist in prioritizing candidate genes discovered in a linkage analysis, Positional Medline (PosMed) executes a full-text search of documents given a query word input and ranks the positional cloning candidate genes based ...
website       summary

PostgreSQL
PostgreSQL is a sophisticated Object-Relational DBMS, supporting almost all SQL constructs, including subselects, transactions, and user-defined types and functions. It is the most advanced open-source database available anyw...
website       summary

POV-Ray
Persistence of Vision Raytracer; use in conjunction with Swiss-PdbViewer to create graphics for presentation and publication.
website       summary

POWER
The Phylogenetic Web Repeater (POWER) allows users to perform phylogenetic analysis using the PHYLIP package. The POWER pipeline can start with processing either multiple sequence alignments (MSA) or can proceed directly with...
website       summary

POXO
POXO is a series of tools that can be used to discover, search and verify possible regulatory cis-element(s) from set(s) co-expressed genes.
website       summary

Poxvirus Bioinformatics Resource Center
Includes poxvirus genomic sequences; annotation and analysis of poxvirus genes; web-based data mining and sequence analysis tools; software for analysis of complete genomes; literature resource; repository of poxvirus species...
website       summary

PPG
The Protein Picture Generator (PPG) is a tool for making pictures (and animations) of protein structures from PDB files.
website       summary

PPISearch
PPISearch is a web server for identification of homologous protein-protein interactions (PPIs), inferring transferability of interacting domains and functions of a query protein pair. Homology is searched across multiple spec...
website       summary

Practical Structural Databases
Detailed compendium of links to structure databases, viewers, tools.
website       summary

PRALINE
Praline is a multiple sequence alignment program that can integrate information from sequence similarity searches and secondary structure prediction.
website       summary

PrDOS
PrDOS (Protein Disorder Prediction Server) is a server to predict the disordered regions of a protein from its amino acid sequence.
website       summary

PreBI
Prediction of Biological Interfaces (PreBI) is a server for predicting protein-protein interfaces in protein structures that maximizes both the degree of complementarity and the interface area.
website       summary

PrecisePrimer
PrecisePrimer is an easy to use web server for designing PCR primers for DNA library cloning and DNA shuffling.
website       summary

PRED-GPCR
PRED-GPCR is a tool which queries user-supplied sequences against a database of HMMs corresponding to G-protein coupled receptor (GPCR) families in order to determine which GPCR family the query sequence most resembles.
website       summary

PredHS
PredHS (Prediction of Hot Spots) is a computational method that can effectively identify hot spots on protein-protein interaction interfaces by using optimally structural neighborhood properties.
website       summary

PredictProtein
PredictProtein is a protein sequence analysis and structure prediction tool. Users provide a protein sequence, and PredictProtein reports similar sequences, PROSITE sequence motifs, and various types of structure prediction i...
website       summary

PredictProtein
PredictProtein is a web server for prediction of annotation of protein function and structure from protein sequence.
website       summary

PredictRegulon
PredictRegulon is a tool that, for a given regulatory protein and prokaryotic genome, predicts binding sites and operons. The user selects a prokaryote genome and provides an ungapped multiple sequence alignment representing ...
website       summary

Predikin
The Predikin web server allows users to predict substrates of protein kinases. Users input a protein kinase for evaluation
website       summary

PrediSi
PrediSi (Prediction of Signal Peptides) takes one or more amino acid sequences as input and predicts the likelihood that they are signal peptides as well as their cleavage positions. It can be used to analyse whole proteome d...
website       summary

PREDITOR
PREDITOR predicts torsion angles in proteins from NMR chemical shift data and sequence homology. PREDITOR combines sequence alignment methods with advanced chemical shift analysis techniques to generate its torsion angle pred...
website       summary

PRED-TMBB
PRED-TMBB is a tool that takes a Gram-negative bacteria protein sequence as input and predicts the transmembrane strands and the probability of it being an outer membrane beta-barrel protein. The user has a choice of three di...
website       summary

PredUs
PredUs is a web server for the prediction of protein-protein interfaces. The method predicts protein-protein interfaces of a given monomeric query protein using its close and remote structural neighbors.
website       summary

PREP Suite
The PREP (Predictive RNA Editors for Plants) suite predicts sites of RNA editing based on the principle that editing in plant organelles increases the conservation of proteins across species. Predictors for mitochondrial gene...
website       summary

PREX
PREX is a database of peroxiredoxin (Prx or PRDX) protein sequences unambiguously classified into one of six distinct subfamilies. Subfamily members were identified using the Deacon Active Site Profiler (DASP) bioinformatics ...
website       summary

PRI-CAT
PRI-CAT is a web-based workflow tool for the management and analysis of plant ChIP-seq experiments, with focus on Arabidopsis. Secondary analysis can be performed with the aid of GALAXY.
website       summary

PRIDB
The Protein-RNA Interface Database (PRIDB) is a database of protein-RNA interfaces extracted from complexes in the Protein Data Bank (PDB). It is designed to facilitate detailed analyses of individual protein-RNA complexes an...
website       summary

PRIDE
The Proteomics Identifications database (PRIDE) is a repository of mass spectrometry-derived proteomics data. Several new and improved features in PRIDE have been introduced, including direct submission of fragment ion annota...
website       summary

PriFi
PriFi is a tool for designing and evaluating primer pairs based on the input of a DNA sequence alignment; useful for the PCR amplification of homologs.
website       summary

Primaclade
Primaclade accepts a multiple species nucleotide alignment file as input, iteratively runs the Primer3 application for each sequence, and then collates the results to identify a set of polymerase chain reaction (PCR) primers ...
website       summary

Primer3
Comprehensive PCR primer and hybridization probe design tool; many options but easy to accept defaults at first.
website       summary

Primer3Plus
Primer3Plus is an enhanced web interface to the popular Primer3 PCR primer design program.
website       summary

PrimerBank
PrimerBank is a public resource for the retrieval of human and mouse primer pairs for gene expression analysis by PCR and Quantitative PCR (QPCR). Information on these primers such as T(m), location on the transcript and ampl...
website       summary

primers4clades
Primers4clades is a web server that uses phylogenetic trees to design primers to amplify novel sequences from across species using metagenomic DNA or from uncharacterized organisms. Beginning with a set of non-aligned protein...
website       summary

PrimerStation
PrimerStation is a multiplex genomic PCR primer design tool specific for the human genome.
website       summary

Primer Z
Primer Z is an interface for PCR primer design for human, mouse, or rat genes and human SNPs; uses Primer3 primer design program.
website       summary

PRISM
PRISM (PRotein Interactions by Structural Matching) is a tool for analysing protein interfaces and predicting protein-protein interactions.
website       summary

PRISM
PRISM is a web server and repository for prediction of protein-protein interactions and modeling their 3D complexes.
website       summary

ProbeLynx
Using current releases of genomic sequence data, ProbeLynx allows users to assess the specificity of probe sequences used for microarray experiments. The user provides probe sequences in FASTA or tab-delimited format, and Pro...
website       summary

ProBiS
Protein Binding Sites (ProBiS) is a web server which detects protein binding sites based on local structural alignments. Algorithms have been parallelized to allow for faster computing against the PDB. Pre-calculated protein ...
website       summary

ProBiS-ligands
ProBiS is a web server for predicting ligands by similarity in binding sites.
website       summary

ProCKSI
ProCKSi (Protein Structure Comparison, Knowledge, Similarity and Information) is a multi-layer protein comparison meta-server that computes structure similarities using various information theory measures. ProCKSI integrates ...
website       summary

PRODOC
PRODOC is a repository of domain assignments from Pfam for proteins encoded in different complete genomes and a tool for querying this information.
website       summary

ProdoNet
A web-based application for the mapping of prokaryotic genes and the corresponding proteins to common gene regulatory and metabolic networks. Users input a list of genes from which shared operons, co-expressed genes and share...
website       summary

ProfCom
Profiling of complex functionality (ProfCom) is a web based tool for the interpretation of genes that were identified to be functionally linked. Combinations of annotation terms are used to profile complex functions.
website       summary

PROFEAT
Protein Features (PROFEAT) is a tool for computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence. New functions include computation of protein-protein and protein-smal...
website       summary

PROFtmb
PROFtmb predicts transmembrane beta-barrel (TMB) proteins in Gram-negative bacteria. In addition to running your own predictions, you can also download predictions for all proteins in 78 Gram-Negative bacterial genomes.
website       summary

ProFunc
ProFunc takes a PDB-format structure as input and predicts the likely function of the protein based on various sequence and structural analysis methods.
website       summary

ProGMap
Protein Group Mappings (ProGMap) facilitates the annotation of newly sequenced proteins by helping users assess the coherence of protein groups found in various databases. ProGMap is based on a non-redundant dataset of over 6...
website       summary

Projector 2
Projector 2 allows users to map completed portions of the genome sequence of an organism onto the finished (or unfinished) genome of a closely-related species or strain. Using the related genome sequence as a template can fac...
website       summary

ProKware
ProKware is a tool for investigating protein structural properties such as domains, functional sites, and post-translational modifications. To use some features a stand-alone piece of software is necessary; currently availabl...
website       summary

PROMALS and PROMALS3D
PROMALS (Profile Multiple Alignment with Local Structure) is a progressive mutliple sequence alignment method that improves alignment quality by using additional homologs from PSI-BLAST searches and secondary structure predic...
website       summary

ProMateus
ProMateus extends ProMate, a protein binding site predictor, and allows the user to suggest new features that might improve the prediction of the binding site locations.
website       summary

PromH
PromH predicts transcription start sites (TSS), TATA boxes, and transcription factor binding sites (TFBS) in promoter regions using pairs of orthologous sequences.
website       summary

PROMISCUOUS
PROMISCUOUS is a database of drugs, including withdrawn or experimental drugs, annotated with drug-protein and protein-protein relationships compiled from public resources via text and data mining including manual curation. M...
website       summary

PromoSer
Server which aims to extract proximal promoter sequences from mammalian genomes. Does so by mapping mRNA and EST sequences and tracking overlapping alignments to find the transcription start site.
website       summary

ProMoST
ProMoST (Protein Modification Screening Tool) is a program to calculate accurate MW and pI values from proteins considering the effects of post-translational modifications. Results are displayed as calculated values of pI and...
website       summary

PromoterPlot
PromoterPlot takes the output from a TransFac search as input, and finds similarities between groups of promoters in an attempt to simplify the results of transcription factor searches. FASTA/Affymetrix IDs can also be used a...
website       summary

PromoterWise
Compares two DNA sequences allowing for inversions and translocations, ideal for promoters.
website       summary

ProSAT2
Protein Structure Annotation Tool (ProSAT2) is a tool for the visualization of sequence based, residue-specific annotations mapped onto three-dimensional (3D) protein structures
website       summary

ProSA-web
ProSA-web (Protein Structure Analysis) is an extension of the classic ProSA program used for the refinement and validation of experimental protein structures and in structure prediction and modeling.
website       summary

PROSESS: A Protein Structure Evaluation Suite and Server
PROSESS (PROtein Structure Evaluation Suite and Server) is a comprehensive web server designed to evaluate and validate protein structures generated by X-ray crystallography, NMR spectroscopy and computational modeling.
website       summary

ProSight PTM
ProSight PTM allows identification and characterization of intact proteins and their post- translational modifications (PTMs) using data from the \'Top-Down\' tandem mass spectrometry (MS/MS) approach.
website       summary

PROSITE
Database of protein families and domains defined from SwissProt database; consider also checking specific motif databases such as PhosphoBase.
website       summary

PROSITE
PROSITE consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. PROSITE is used for the annotation of domain features of UniPr...
website       summary

ProSMoS
ProSMoS facilitates protein structure patterns searches. The web program converts 3D structures into an interaction matrix model including such details as the secondary structural element (SSE) type, handedness of connections...
website       summary

PROSPECT-PSPP
An automated Protein Structure Prediction Pipeline (PSPP) based on multiple structure prediction tools. A key component of the pipeline is the fold recognition program, PROSPECT. Server supports genome scale analyses.
website       summary

Prospectr
Prospectr (PRiOrization by Sequence & Phylogenetic Extent of CandidaTe Regions) can be used to enrich lists of genes found at a suspected disease locus. Given a list of genes, Prospectr will return a ranked list ordered by th...
website       summary

ProSplicer
Database which stores alternative splicing information generated from EST, mRNA and protein alignments with genomic sequence; text-based queries and graphical views of putative splice variants.
website       summary

ProtCID
The protein common interface database (ProtCID) is a database that contains clusters of similar homodimeric and heterodimeric interfaces observed in multiple crystal forms (CFs). In ProtCID, protein chains in the protein data...
website       summary

ProteDNA
ProteDNA identifies the sequence-specific binding residues in a transcription factor, protein-DNA interaction.
website       summary

Protegen
Protegen is a web-based database and analysis system that curates, stores and analyzes protective antigens. Protegen includes basic antigen information and experimental evidence curated from peer-reviewed articles. It also in...
website       summary

ProteinCCD
Protein Crystallographic Construct Design (Protein CCD) is a meta-web server that facilitates the design of several truncated constructs of a protein using experimental data or sequence analysis tools. From input DNA sequence...
website       summary

ProteinDBS
ProteinDBS takes a PDB ID or structure as input, and searches for similar protein tertiary structures using computer visualization techniques. The superposition of structures and the aligned component of the sequence can then...
website       summary

Protein Dipole Server
The Protein Dipole server calculates and displays the net charge, dipole moment and mean radius of any 3-dimensional protein structure.
website       summary

Protein Geometry Database
The Protein Geometry Database (PGD) enables biologists to easily and flexibly query information about the conformation alone, the backbone geometry alone, and the relationships between them. The PGD is valuable for assessing ...
website       summary

Protein Naming Utility
The Protein Naming Utility (PNU) is a web-based database for storing and applying naming rules to identify and correct syntactically incorrect protein names, or to replace synonyms with their preferred name. The PNU allows us...
website       summary

The Protein Ontology
The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. PRO now includes representations ...
website       summary

ProteinProspector
Various tools used for sequence database mining in connection with mass spectrometry experiments.
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Proteios - The Open Source Proteomics Initiative
Proteios is an initiative to create an open-source storage, analysis and organization system for proteomics experiments.
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Protemot
The Protein motif (Protemot) server predicts protein binding sites based on structural templates automatically extracted from crystal structures of protein-ligand complexes in the PDB.
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Proteome Analyst
Proteome Analyst is a high-throughput tool for predicting properties for each protein in a proteome. The user provides a proteome in fasta format, and the system employs Psi-blast, Psipred and Modeller to predict protein func...
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ProTeus
ProTeus (Protein Terminus) is an archive of functional signatures in protein termini
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PROTEUS2
PROTEUS2 is a web server for comprehensive protein structure prediction and structure-based annotation. The analysis pipeline includes signal identification, trans-membrane helix prediction, trans-membrane beta-strand predict...
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Protinfo
Protinfo takes a protein sequence as input and returns the atomic coordinates for a prediction of tertiary structure for that protein. Predictions can be made by comparative or de novo modelling.
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Protinfo PPC
Protinfo Prediction of Protein Complex (PPC) is a web server that predicts atomic level structures of interacting proteins from their amino acid sequences.
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ProTox
ProTox is a web server for the in silico prediction of oral toxicities of small molecules in rodents.
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ProtParam
Compute molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity.
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ProtTest
ProtTest is a program that determines the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment.
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PROWL
Software tools and integrated databases to facilitate analyzing the output from protein mass spectrometry experiments.
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PRUNE and PROBE
PRUNE is a web server for the selection of a subset of protein-protein docking poses generated during sampling search using an interface area based edge-scoring function. PROBE is a web server for refining, scoring and rankin...
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(PS)2 Protein Structure Prediction Server
(PS)2 Protein Structure Prediction Server performs automated homology modeling by combining PSI-BLAST, IMPALA, and T-Coffee for template selection and target-template alignment. The final three-dimensional (3D) structure is b...
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PSA
Prediction of probable secondary structures and fold-class; good for visualizing amphipathic helices, where present.
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Pscan
Pscan is a web server scans a set of sequences to find over-represented transcription factor binding site motifs within co-regulated or co-expressed genes.
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PseudoCAP
Pseudomonas aeruginosa community annotation project (PseudoCAP); information and tools for genome analysis and annotation of P. aeruginosa.
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Pseudomonas Genome Database
The Pseudomonas Genome Database integrates completely-sequenced Pseudomonas genome sequences and their annotations with genome-scale, high-precision computational predictions, experimental data, and manually curated, communit...
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Pseudomonas Genome Project
This is a comprehensive database on all Pseudomonas species genomes providing primarily access to Pseudomonas aeruginosa genomic data and annotation. Its interface faciliates comparative analyses of genes, proteins, annotatio...
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PSEUDOVIEWER
PSEUDOVIEWER is a tool for visualizing RNA pseudoknot structures.
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PSIPRED
An excellent tool for prediction of secondary structure, with access to GenTHREADER for protein fold recognition and MEMSAT-2 transmembrane topology prediction.
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PSORTdb
PSORTdb is a database of proteins of experimentally known (ePSORTdb) and computationally predicted (cPSORTdb) subcellular localization.
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PSORTdb
PSORTdb (part of the PSORT family) is a database of protein subcellular localizations for bacteria and archaea that contains both information determined through laboratory experimentation (ePSORTdb dataset) and computational ...
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PSORT.org
PSORT.org provides links to the PSORT family of web-based programs for subcellular localization prediction, including PSORTb and WoLF PSORT, well as other datasets and resources relevant to localization prediction.
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psRNATarget
psRNATarget is a plant small RNA target analysis server which features reverse complementary matching between small RNA and target transcript, and target site accessibility evaluation. It is designed for high-throughput analy...
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PSSRdb
PSSRdb (Polymorphic Simple Sequence Repeats database) is a relational database of polymorphic simple sequence repeats (PSSRs) extracted from different species of prokaryotes. This database gives useful information such as loc...
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pssRNAMiner
pssRNAMiner is a web server which identifies trans-acting siRNA clusters in plants, as well as their potential phase initiators. Users input a small RNA dataset and specify a transcript-genomic library for mapping.
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pTARGET
pTARGET predicts the subcellular localization of eukaryotic proteins based on the occurrence patterns of location-specific protein functional domains and the amino acid compositional differences in proteins from nine distinct...
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PTGL
Protein Topology Graph Library (PTGL) is a database on protein secondary structure topologies, including search facilities, the visualization as intuitive topology diagrams as well as in the 3D structure, and additional infor...
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PTHGRN
PTHGRN is a web server for unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data.
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PubChem
The PubChem BioAssay database is a public repository for biological activities of small molecules and small interfering RNAs (siRNAs). It archives experimental descriptions of assays and biological test results. A PubChem Bio...
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PubChem BioAssay Service
PubChem BioAssay Service expands upon PubChem. It is a set of web servers which provide for rapid data retrieval, integration, and comparison of biological screening results, exploratory structure-activity analysis and target...
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PubCrawler
It goes to the library. You go to the pub; receive email alerts for current contents of PubMed and GenBank; e.g. use accession number of htg record as query to receive sequence updates (as the version number changes).
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PubGene
Searchable literature network of human genes with tools for gene expression analysis. Choose from the free public service, or purchase the commercial package.
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Public Library of Science
The Public Library of Science (PLoS) is a non-profit organization of scientists and physicians committed to making the world\'s scientific and medical literature a freely available public resource.
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PubMed
Entrez-searchable database of biomedical literature citations with links to molecular resources at the NCBI.
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PubMed Central
PubMed Central (PMC) is the U.S. National Institutes of Health (NIH) free digital archive of biomedical and life sciences journal literature.
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PubServer
PubServer collects homologous sequences from NR database and retrieves and filters associated publications.
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PUDGE
PUDGE is a protein structure prediction server. Modeling is divided into 5 stages: template selection, alignment, model building, model refinement and model evaluation.
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PupaSuite
PupaSuite is a SNP analysis tool that allows for the selection of relevant SNPs within a gene based on the characteristics of the SNP. PupaSuite also provides information about LD parameters (based on genotype data from HapMa...
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Puzzleboot
Puzzleboot is a UNIX shell script facilitating bootstrap analysis using TREE-PUZZLE and PHYLIP. It enhances TREE-PUZZLE by allowing one to analyse multiple datasets, and can be used for both protein and DNA distance bootstrap...
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PVS
Protein Sequence Variability (PVS) is a web server for the prediction of conserved T-cell epitopes. Several variability metrics are used to compute the absolute site variability in multiple protein sequence alignments.
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PyMOL
PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations.
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Qgrid
Server which provides cluster tree diagrams of a protein based on the charged atoms or hydrophobicity of each of its residues. The diagram allows for visual inspection of the distribution of hydrophobic and charged regions in...
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QGRS Mapper
Quadruplex forming G-Rich Sequences (QGRS) Mapper searches nucleotide sequences for the presence of G-quartet motifs. QGRS Mapper allows you to view the distribution and composition of QGRS in the context of alternatively spl...
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QMEAN
QMEAN is a web server for protein model quality estimation. Either the composite scoring function QMEAN or the clustering based scoring function QMEANclust may be used.
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QSCOP - BLAST
QSCOP-BLAST is a service that uses BLAST to search the QSCOP (Quantitative SCOP) server, an extension of classic SCOP (Structural Classification of Proteins).
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QuadFinder
QuadFinder is a tool for the identification and analysis of quadruplex forming nucleotide sequences.
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Quadruplex
A website to serve the quadruplex community. Contains conference information, forums, database and parsers.
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QuasiMotiFinder
QuasiMotiFinder uses physicochemical similarity to PROSITE motifs and evolutionary conservation to predict sequence locations with possible function (pseudo-motifs).
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A Quick Guide To Sequenced Genomes
The Quick Guide includes descriptions of more than 150 organisms and has links to sequencing centers and scientific abstracts.
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QuickSNP
QuickSNP is a resource for the selection of tagSNPs in the human genome that includes a gene-centric selection module.
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QUMA
Quantification tool for Methylation Analysis (QUMA) is a web-based bisulfite sequencing analysis tool for CpG methylation analysis. Following user input of PCR target genomic sequence and raw bisulfite sequences, alignment, v...
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R
System for statistical computation and graphics; an interpreted computer language which allows branching and looping as well as modular programming using functions.
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R. S. WebTool
R. S. WebTool is a web server for random sampling-based significance evaluation of pairwise distances.
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R3D-BLAST
R3D-BLAST is a BLAST-like search tool that allows users to quickly search against the PDB for RNA structures sharing similar substructures with a specified query RNA structure. Input is an RNA 3D structure in PDB format; outp...
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RACE
RACE (Remote Analysis Computation for gene Expression data) is a collection of web tools designed to assist with the analysis of DNA microarray data and results.
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RADAR
RADAR (RNA Data Analysis and Research) provides multiple tools for RNA structure analysis including: pairwise structure alignment, multiple structure alignment, constrained structure alignment, database searching, and predict...
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RAPIDO
RAPIDO conducts 3D alignments of crystal structures of different protein molecules in the presence of conformational change.
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RasMol
3-D structure viewer, web browser helper application.
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RASMOT-3D PRO
The RASMOT-3D PRO web server performs systematic searches in 3D protein structures for a set of residues exhibiting a particular topology. Input is a PDB file for the motif of interest; output is an interactive list of protei...
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RASS
RASS is a webserver for RNA alignment in the joint sequence-structure space.
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Rat Genome Database (RGD)
The Rat Genome Database (RGD) is a repository of rat genetic and genomic data. As well as integrating this data with mapping, physiological and strain information, RGD also provides researchers with several tools that facilit...
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RbDe
Residue-based Diagram editor (RbDe) constructs schematic diagrams of protein sequences to help observe the topology of secondary structure and transmembrane regions; free registration is required to use all features.
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RBPDB
The RNA-Binding Protein DataBase (RBPDB) is a collection of experimental observations of RNA-binding sites, both in vitro and in vivo, manually curated from primary literature. The database is accessible by a web interface wh...
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RBPmap
RBPmap is a web server for mapping binding sites of RNA-binding proteins.
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RCI
RCI (Random Coil Index) is a method for predicting protein flexibility using secondary chemical shifts.
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R-Coffee
The R-Coffee web server uses pairwise or multiple sequence alignment methods to produce multiple alignments of non-coding RNA sequences, incorporating predicted or known secondary structures.
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RCSB Protein Data Bank
The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and adv...
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Reactome
Reactome is a database of human biological pathways and processes ranging from basic processes of metabolism to complex regulatory pathways. The data is curated by biologists and subsequently peer-reviewed for accuracy and co...
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ReadOut
Readout is a server for the calculation of direct and indirect readout energy Z-scores which estimate the degree of sequence specificity of the protein-DNA complex. Readout can be useful for checking the quality of protein-DN...
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ReadSeq
Sequence format conversion; includes GenBank, EMBL, GCG, FASTA, ASN.1, Phylip and others.
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REBASE
REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced infor...
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Recode
Recode2 is a database of genes that utilize non-standard translation for gene expression purposes. Recoding events described in the database include programmed ribosomal frameshifting, translational bypassing (aka hopping) an...
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RECON
RECON is a tool for calculating the probability of nucleosome formation along a DNA sequence input by the user.
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R.E.D.
R.E.D. Server is designed to build force field libraries for new molecules and molecular fragments. One can derive molecular electrostatic potential-based atomic charges embedded in force field libraries for use in force fiel...
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REDfly
Regulatory Element Database for Drosophila (REDfly) is a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs). REDfly seeks to include all experimentally verified fly CRMs along with their DNA ...
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REDfly
The REDfly database of Drosophila transcriptional cis-regulatory elements provides experimentally validated cis-regulatory modules and transcription factor binding sites. The user interface is designed for access by both caus...
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REDUCE
REDUCE uses a motif-based regression method for the identification of TFBS (transcription factor binding sites) from microarray data in yeast, worm and fly. A free registration is required.
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RegAnalyst
RegAnalyst is a web server that integrates MoPP (Motif Prediction Program), MyPatternFinder and MycoRegDB (mycobacterial promoter and regulatory elements database).
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RegPhos
RegPhos is a database for exploration of the phosphorylation network associated with an input of genes/proteins. Subcellular localization information is also included.
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RegPrecise
The RegPrecise database was developed for capturing, visualization and analysis of predicted transcription factor regulons in prokaryotes that were reconstructed and manually curated by utilizing the comparative genomic appro...
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RegPredict
RegPredict web server provides comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics.
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RegRNA
Regulatory RNA (RegRNA) is a server for identifying regulatory RNA motifs and elements in mRNA sequences including: motifs located in the 5\'-UTR and 3\'-UTR; motifs involved in mRNA splicing and transcriptional regulation; o...
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RegulonDB
RegulonDB is a reference database of Escherichia coli K-12. Transcriptional regulation is now part of a unit that initiates with the signal and continues with the signal transduction to the core of regulation, modifying expre...
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ReMus
REinforced Merging techniques for Unique peptide Segments (ReMus) is designed for identification of the locations and compositions of unique peptide segments from a set of protein family sequences.
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REPAIRtoire
REPAIRtoire is a database resource for systems biology of DNA damage and repair. The database collects and organizes the following types of information: (i) DNA damage linked to environmental mutagenic and cytotoxic agents, (...
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RepeatMasker
Screens a DNA sequence against a library of repetitive elements; returns a masked query sequence and a table annotating the masked regions.
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REPK
REPK (Restriction Endonuclease Picker) assists in the choice of restriction endonucleases for terminal restriction fragment length polymorphism (T-RFLP) by finding sets of four restriction endonucleases which together uniquel...
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REPPER
REPPER (REPeats and their PERiodicities) is a tool for detecting and analysing regions in protein sequences or sequence alignements that have short gapless repeats.
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REPRO
REPRO web server is able to recognise distant repeats in a single query sequence.
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RepTar
RepTar is a database of miRNA target predictions, based on the RepTar algorithm that is independent of evolutionary conservation considerations and is not limited to seed pairing sites.
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Rescue-ESE
Server for the identification of hexnucleotide exonic splicing enhancers (ESEs). Also contains a list of 238 identified ESEs for human genes.
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ResponseNet
ResponseNet is a network optimization approach for revealing signaling and regulatory networks linking genetic and transcriptomic screening data. Users upload weighted lists of proteins and genes.
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RevTrans
RevTrans takes a set of DNA sequences, virtually translates them, aligns the peptide sequences, and uses this as a scaffold for constructing the corresponding DNA multiple alignment.
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Rfam
Database of structure-annotated multiple sequence alignments, covariance models and family annotation for a number of non-coding RNA families.
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Rfam
The Rfam database aims to catalogue non-coding RNAs through the use of sequence alignments and statistical profile models known as covariance models.
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RF_DYMHC
RF_DYMHC (Random Forest-Based System for Detecting Yeast Meiotic Recombination Hotspots and Coldspots) predicts recombination hot/cold spots in the yeast genome.
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RHYTHM
RHYTHM predicts buried vs. exposed residues of helical membrane proteins. Users input either primary, secondary or tertiary structure information. Output includes secondary structure and topology information, and the contact ...
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RibEx
Riboswitch Explorer (RibEx) searches sequences for known riboswitches and also for predicted bacterial regulatory elements that are highly conserved
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Ribosomal Database Project
Highly curated database of aligned and annotated rRNA sequences with accompanying phylogenies; data available for download.
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Riboswitch finder
RNA motif search program that identifies RNA motifs called riboswitches which are metabolic binding domains in mRNA that regulate gene expression. The program was originally designed around a set of riboswitches found in Baci...
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RiceXPro
RiceXPro is a gene expression database to provide the transcriptional changes throughout the growth of the rice plant in the field. RiceXPro contains two data sets corresponding to spatiotemporal gene expression profiles of v...
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RIKEN integrated database of mammals
The RIKEN integrated database of mammals integrates not only RIKEN's original databases, such as FANTOM, the ENU mutagenesis program, the RIKEN Cerebellar Development Transcriptome Database and the Bioresource Database, but a...
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rMotif
rMotif provides tools for the discovery of de-novo, fully, or partially characterized regulatory motifs including transcription factor binding sites (TFBS).
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RNA Analyzer
RNA Analyzer searches for known structures and identifies RNA motifs in your input sequence.
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RNABindR
RNABindR is a server for analyzing and predicting RNA binding sites in proteins.
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RNAbor
RNAbor is a server for computing structural neighbors of a RNA secondary structure.
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RNAfold
Predict RNA secondary structure from sequence; note sequence length limit.
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RNA folding Servers
List of RNA folding servers and related web sites maintained by Herve Isambert.
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RNA helicase database
The RNA helicase database integrates information on RNA helicases. The database allows retrieval of comprehensive information on sequence, structure and on biochemical and cellular functions of all RNA helicases from the most...
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RNAhybrid
RNAhybrid is a tool for predicting miRNA (microRNA) targets by calculating the minimum free energy of hybridization between target RNA and miRNA sequences.
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RNA Informatics Links
An exhaustive list of RNA links; from the experts in the Major lab.
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RNALogo
RNALogo is a tool for graphical representation of features within multiple RNA sequence alignments and their consensus RNA secondary structures. Each RNA family in Rfam has been graphically evaluated for a logo.
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RNALOSS
RNALOSS (RNA locally optimal secondary structure) is a tool for the computation of locally optimal secondary structures.
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RNAmmer
RNAmmer predicts genes for ribosomal RNA (rRNA) in full genome sequences using hidden Markov models trained on data from the 5S ribosomal RNA database and the European ribosomal RNA database project.
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The RNA Modification Database, RNAMDB
The RNA Modification Database (RNAMDB) contains information pertaining to naturally occurring RNA modifications. The database employs an easy-to-use, searchable interface for obtaining detailed data on the 109 currently known...
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RNAMOT
RNA motif search program; not a Web-tool.
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RNA Movies
RNA Movies is a tool for the visualization of RNA secondary structure spaces. The program creates an interpolated animation of user provided sets of secondary structure data.
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RNAMST
RNA Motif Search Tool (RNAMST) is a tool for identifying homologs of a pre-defined RNA structural motif among numerous RNA sequences.
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RNAmutants
A web server to explore the effect of mutations on the RNA secondary structures.
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RNAmute
RNAmute is a web server to facilitate mutational analysis of RNA secondary structures. Single point and multi-point mutations are handled.
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RNApdbee
RNApdbee is a web server for deriving secondary structures from PDB files of knotted and unknotted RNAs.
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RNApredator
RNApredator is a web server for the prediction of bacterial sRNA targets. The user can choose from a large selection of genomes. Accessibility of the target to the sRNA is considered.
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RNAsoft
Software for RNA/DNA secondary structure prediction and design
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RNA Studio
RNA Studio contains software for RNA analyses including tools for structure prediction, comparison, and visualization.
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The RNA World
An RNA resource hub.
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RNAz
RNAz detects functional RNA secondary structures in multiple sequence alignments based on thermodynamic stability and structural conservation.
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Robetta
The Robetta server provides protein structure prediction tools and interface alanine scanning. The structure prediction is accomplished by either comparative modelling or the de novo Rosetta fragment insertion method. Interfa...
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RosettaAntibody
The RosettaAntibody server predicts the structure of an antibody variable region given the amino acid sequences of the light and heavy chains. 2000 independent structures are generated and scored, with the top 10 models being...
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RosettaBackrub
The RosettaBackrub server computes near-native conformational ensembles from a single input protein structure in PDB format using the Backrub method.
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RosettaDesign
RosettaDesign identifies low energy sequences for specified protein three dimensional (3D) structures and can been used to predict stable side chain conformations.
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RosettaDock Server
RosettaDock server is a structure prediction program that searches the rigid body and side chain conformational space of two interacting proteins to find a minimum free-energy complex for the protein-protein interaction struc...
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Rosetta FlexPepDock
Rosetta FlexPepDock web server is a high resolution peptide docking protocol for modeling of peptide-protein complexes.
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RPBS
Ressource Parisienne en Bioinformatique Structurale (RPBS) is a structural bioinformatics resource with several types of specific services including tools for searching sequence (AUTOMAT) and structure (YAKUSA) databases and ...
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rQuant.web
rQuant.web is a web service for quantitative analysis of RNA sequencing data based on quadratic programming. rQuant.web is available as a tool in Galaxy.
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RSAT
Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random s...
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rSNP_Guide
a system of databases documenting the influence of mutations in regulatory gene regions
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R spider
R spider is a web tool for the analysis of a gene list using the systematic knowledge of core pathways and reactions from KEGG and Reactome.
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RSSsite
RSSsite consists of a reference database and prediction tool for the identification of cryptic recombination signal sequences (RSSs) in the human and mouse genomes.
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RTAnalyzer
RTAnalyzer is an application to find new retroposons and detect L1 retroposition signatures.
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RuleGO
RuleGO is a web tool for description of gene groups by means of Gene Ontology. The user is able to describe gene groups on the basis of logical rules that include GO-terms in their premises.
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rVISTA
Server which detects transcription factor binding sites(TFBS) through combining TFBS prediction, sequence comparison and cluster analysis.
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SABBAC
Structural Alphabet based protein Backbone Builder from Alpha Carbon trace (SABBAC) is a tool for the reconstruction of complete protein structures from their alpha-carbon descriptions.
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SAGE Home Page
Serial Analysis of Gene Expression; simultaneous expression and map information.
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SAGEmap
SAGE tag to gene mapping by NCBI.
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SAHG
The Structure Atlas of Human Genome (SAHG) database contains protein structures encoded in the human genome. All open reading frames in the human genome have been subjected to protein structure prediction.
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SAKURA
SAKURA is the DDBJ DNA Database Submission System.
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SALAD
SALAD is a unique comparative genomics database from plant-genome-based proteome data sets. Evolutionarily conserved motifs were extracted by MEME software from protein-sequence annotation groups selected by BLASTP from the p...
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SALAMI
The SALAMI web server searches the protein data bank (PDB) for structures similar to input coordinates of a protein chain. Output is provided in a simple structure viewer with details of the sequence, structural similarity an...
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SA-Mot
SA-Mot is a wbe server for the extraction and location of structural motifs of interest from protein loops. Recurrent and conserved structural motifs involved in structural redundancy of loops are considered.
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SAPS - Statistical Analysis of Protein Sequences
Calculations include compositional analysis, charge distribution, identification of highly hydrophobic (transmembrane) segments, sequence repeats, and more.
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SARA
Based on the SARA program, the SARA server computes pairwise alignment of RNA structures for structure based assignment of RNA function. The server can also be used for RNA pairwise structure alignment.
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SARA-Coffee
SARA-Coffee is a web server for aligning RNA sequences using tertiary structure.
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SA-Search
SA-Search is a tool which first converts a PDB structure file into a one-dimensional representation using a structural alphabet, and then searches for similarities using standard methods for sequence alignment.
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SATCHMO-JS
SATCHMO-JS is a web server for simultaneous estimation of protein multiple sequence alignments and phylogenetic trees. Input is a FASTA file of sequences, and output is a phylogenetic tree and multiple sequence alignment.
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Satellog
Satellog is a database for the identification and prioritization of satellite repeats in disease association studies.
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SBSPKS
SBSPKS contains web tools for structure based sequence analysis of polyketide synthases. Model_3D_PKS for modeling, visualization and analysis of 3D PKS catalytic domains; Dock_Dom_Anal for identification of key interacting r...
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SBT Interface - dbMHC
The SBT (Sequencing-based typing) interface is a tool accompanying the NCBI's Major Histocompatibility Complex database (dbMHC). It identifies the allelic composition of sequence-based typing (SBT) results of cDNA or gen...
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ScanACE
Scans for Nucleic Acid Conserved Elements scans DNA sequence for over-represented oligomers to find elements which match a DNA motif; free for non-commercial use with license agreement.
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ScanAlyze, Cluster, TreeView
Eisen Lab software for microarry image processing, analysis and visualization; available for download to windows platforms only; free with registration for non-commercial use.
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SCANMOT
SCANMOT is a sequence similarity searching tool that adds the additional constraints of simultaneous matching of multiple motifs.
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ScanProsite
ScanProsite is a tool for detecting PROSITE signature matches in protein sequences. Users can also search protein databases for specific motifs.
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SCANPS
SCANPS is a web server for iterative protein sequence database searching by dynamic programming. Sensitivity and selectivity outperform PSI-BLAST. The server allows a range of different protein sequence databases to be search...
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Scansite
Scansite searches for motifs within proteins that are likely to be phosphorylated or that bind to common cellular signaling domains.
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The Scientist
News journal for the life scientist.
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SCit
SCit is a set of tools facilitating the analysis and editing of protein side chain conformations. Using a PDB file as input, the tools allow the user to perform such tasks as listing and/or modifying the values of the dihedra...
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SCLD
The Stem Cell Lineage Database (SCLD) user-editable lineage maps illustrating both endogenous development and the directed differentiation of human and mouse embryonic stem cells.
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SCMD
The Sacharomyces Cerevisiae Morphological Database (SCMD) is a collection of micrographs of budding yeast mutants; visualization and data mining tools are provided.
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Scooby-domain
Scooby-domain (sequence hydrophobicity predicts domains) is a method to identify globular domains in protein sequence, based on the observed lengths and hydrophobicities of domains from proteins with known tertiary structure.
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SCOP
Structural Classification of Proteins - database created by a combination of manual inspection and automated methods.
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SCOPE
SCOPE (Suite for Computational identification Of Promoter Elements) is a set of programs aimed at identifying novel cis-regulatory elements from groups of upstream sequences. SCOPE does not have any nuisance parameters so doe...
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SCOR
The Structural Classification of RNA (SCOR) is a database designed to provide a comprehensive perspective and understanding of RNA motif structure, function, tertiary interactions and their relationships.
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SCRATCH
SCRATCH is a suite of protein structure software and servers for the prediction of secondary structure, solvent accessibility, disulphide bridges, stability effects of single amino acid mutations, disordered regions, domains,...
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SCR_FIND
SCR_FIND is a tool to analyze structurally conserved regions (SCRs) from superimposed structures and multiple sequence alignments.
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SDM
Site Directed Mutator (SDM) is a web server for predicting effects of mutations on protein stability and function. Users input a wild type structure and the position and amino acid type of the mutation. An environment specifi...
website       summary

SDPMOD
SDPMOD is a comparative modelling tool for small disulfide-bonded proteins (SDPs).
website       summary

SDPpred
SDPpred is a tool for predicting which residues of a protein determine functional differences relative to its homologues. It takes as input an multiple sequence alignment of a protein family divided into groups based on the p...
website       summary

SEA
Serial Expression Analysis (SEA) suite of tools provides a complete resource for the analysis of serial transcriptomic data.
website       summary

SEARCHGTr
SEARCHGTr is a tool for the analysis of glycosyltransferases (GTrs) that allows you to compare a query sequence with the sequences of characterized GTrs.
website       summary

SEARCHPKS
SEARCHPKS is a program for the detection and analysis of Polyketide Synthase (PKS) domains.
website       summary

Seaview
SeaView is a graphical multiple sequence alignment editor that is able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and also to run DOT-PLOT...
website       summary

seeMotif
The web server seeMotif allows users to interactively visualize sequence motifs on protein structures from Protein Data Bank (PDB).
website       summary

Selectome
Selectome is a database of positive selection based on a rigorous branch-site specific likelihood test. Positive selection is detected using CODEML on all branches of animal gene trees. The web interface of Selectome enables ...
website       summary

Selecton
Selecton is a server for the identification of site-specific positive selection and purifying selection.
website       summary

SeLOX
SeLOX web server identifies degenerate lox-like sites within genomic sequences.
website       summary

SelTarbase
The Selective Targets database is a curated database of a growing number of public mononucleotide repeat tracts (MNR) mutation data in microsatellite unstable human tumors. Regression calculations for various microsatellite i...
website       summary

SEM
Symmetry Equivalent Molecules (SEM) is a tool for generating symmetrically equivalent three-dimensional (3D) molecules. This web based tool incorporates the graphics package of RASMOL for visualization; some configuration nec...
website       summary

Semantic-JSON
Semantic-JSON is an approach that provides light-weight access to Semantic Web data. It provides a Representational State Transfer (REST) Web service that retrieves Semantic Web data described in the light-weight JavaScript O...
website       summary

SENT
SENT is a text mining web server. SENT uses non-negative matrix factorization to identify topics in scientific articles associated with an input list of genes.
website       summary

SEPACS
SEPACS (Seroreactivity Pattern Classification System) is a a web-based application for classification of seroreactivity profiles.
website       summary

SEPPA
A computational server for Spatial Epitope Prediction of Protein Antigens (SEPPA) based on a 'unit patch of residue triangle' description of local spatial context in protein surface.
website       summary

SEPPA 2.0
SEPPA 2.0 is a computational server for Spatial Epitope Prediction of Protein Antigens (SEPPA). It describes the local spatial context in a protein surface.
website       summary

SePreSA
SePreSA is a server for the prediction of populations susceptible to serious adverse drug reactions. A drug molecule is submitted to the server and its potential interaction with multiple adverse drug reaction targets is calc...
website       summary

SEQATOMS
SEQATOMS is a web tool for identifying missing regions in PDB sequence. To visualize these regions in their sequence context, a BLAST interface is used that is able to show the lower-case masked regions in the output (hits in...
website       summary

Sequence Harmony
Sequence Harmony detects subfamily specific functional sites from a multiple sequence alignment by scoring compositional differences between given subfamily groupings.
website       summary

SequenceJuxtaposer
SequenceJuxtaposer is a tool for visualizing and comparing biomolecular sequences. Uses a visualization technique called accordion drawing that allows users to zoom into regions of interest in alignments.
website       summary

The Sequence Manipulation Suite 2
The Sequence Manipulation Suite is a set of tools for tasks such as sequence format conversion, sequence presentation, analysing sequence characteristics and shuffling or generating random sequences. It can be accessed over t...
website       summary

The Sequence Ontology Project
The Sequence Ontology Project aims to provide a standard vocabulary for describing biological sequences.
website       summary

Sequin
Desktop tool developed by the NCBI for editing, annotating and submitting DNA sequences to any of the three DNA sequence submission sites (DDBJ, EMBL or GenBank).
website       summary

SeqVISTA
Tool for sequence feature visualization and comparison; integrates with Internet Explorer; accepts GenBank Flat Files, GenBank HTML, FASTA files; plugins exist for visualization of output from RepeatMasker, PsiPred, and Ciste...
website       summary

SerbGO
Searching for the best GO tool (SerbGO) helps users select the GO annotation or list analysis tools which best suit their needs. SerbGO may also be used to compare the capabilities of the various GO tools in the context of th...
website       summary

Servers at University College London
A suite of tools that includes: PSIPRED, a protein structure prediction server; GenTHREADER, for genomic protein fold recognition; MEMSAT2, for transmembrane protein structure prediction; GTD, the genomic threading database; ...
website       summary

SeWeR
Sequence analysis tools on the web; includes nucleic acid, protein, PCR and alignment tools.
website       summary

SFmap
SFmap is a web server for predicting putative splicing factor (SF) binding sites in genomic data. Sequences are input in FASTA format.
website       summary

Sfold
Server with three tools for the rational design of small interfering RNAs (Sirna), antisense oligonucleotides (Soligo), and trans-cleaving ribozymes (Sribo). A fourth tool, Srna, returns output including general folding featu...
website       summary

SGD
The Saccharomyces Genome Database.
website       summary

SGD
The Saccharomyces Genome Database (SGD) is a scientific database for the molecular biology and genetics of the yeast Saccharomyces cerevisiae. The information in SGD includes functional annotations, mapping and sequence infor...
website       summary

sgTarget
sgTarget is a structural genomics resource that helps to select and prioritize good targets for structure determination from a list of sequences. Target selection is based on multiple factors including homology searches and a...
website       summary

SH3-Hunter
SH3-Hunter identifies putative SH3 domain interaction sites on protein sequences.
website       summary

SIB-BLAST
SIB-BLAST is a web server for improved delineation of true and false positives in PSI-BLAST searches using the SimpleIsBeautiful (SIB) algorithm for sequence based homology detection.
website       summary

The SIB Swiss Institute of Bioinformatics
The SIB Swiss Institute of Bioinformatics provides life science databases, tools and support. SIB coordinates research and education in bioinformatics throughout Switzerland and provides high quality bioinformatics services t...
website       summary

siDirect
Server for computing small interfering RNA (siRNA) sequences which are best suited for mammalian RNA interference (RNAi). The site accepts a sequence as input and returns a list of siRNA candidates.
website       summary

SIFT
Sorting Intolerant From Tolerant (SIFT) is a sequence homology-based tool that will predict whether an amino acid substitution will affect protein function.
website       summary

SignalP
Prediction of presence and location of signal peptide cleavage sites in amino acid sequences.
website       summary

Signature
Signature identifies signature genes or genes that are unique to a taxonomic clade and thus useful in phylogenetic analysis. Users input a set of query sequences and returned is a list of taxonomic clades that share signature...
website       summary

SIM4
Align cDNA with genomic DNA, allowing for introns and small number of sequencing errors.
website       summary

SIMAP
The Similarity Matrix of Proteins (SIMAP) database provides a comprehensive and up-to-date pre-calculation of the protein sequence similarity matrix, sequence-based features and sequence clusters. Novel features of SIMAP incl...
website       summary

SIMCOMP/SUBCOMP
SIMilar COMPound (SIMCOMP) computes chemical similarity searches and SUBstructure matching of COMPounds (SUBCOMP) computes chemical substructure searches. Outputs are linked to the KEGG pathway and BRITE databases for interpr...
website       summary

SimGene
SimGene is a collection of freely available molecular biology tools.
website       summary

SiMMap
The SiMMap server statistically derives site-moiety maps which describe the relationship between moiety preferences and the physico-chemical properties of the binding site. Users input the interaction profiles of a query targ...
website       summary

SIREs
SIREs is an iron responsive element prediction tool. From input data, SIREs produces structure analysis, predicted RNA folds, folding energy data and overall quality flags.
website       summary

siRNAdb
This resource includes siSearch, AOSearch, and a siRNAdb which provides a platform for mining an siRNA database, and searching for non-specific matches to your siRNA (small interfering RNAs).
website       summary

siRNA Selection Server
Server aiding the design of short interfering RNAs (siRNAs) by providing information on stability, SNPs and specificity of a potential siRNA.
website       summary

SIRW
SIRW is a web interface to SIR (Simple Indexing and Retrieval System). It combines the ability to search protein/nucleotide databases with keywords and a sequence motif.
website       summary

SITECON
Server for the detection of conformational and physicochemical properties in transcription factor binding sites and potential binding sites.
website       summary

SiteEngine
SiteEngine is a server that searches protein structures for regions that can potentially function as binding sites by scanning for regions on the surface of one protein structure that resemble a specific binding site on the o...
website       summary

SITEHOUND-web
SITEHOUND-web is a server that identifies ligand binding sites in protein structures. Users input a protein structure in PDB format. The program identifies putative ligand binding sites for various favorable probe molecules (...
website       summary

SiteSeer
SiteSeer is a visualization tool for mapping transcription factor binding sites (TFBS) in the upstream regions of single or grouped eukaryotic genes.
website       summary

siVirus
siVirus aids in the design of short interfering RNA (siRNA) and helps to identify conserved target sequences for antiviral RNA interference.
website       summary

SledgeHMMER
SledgeHMMER is a tool for searching the Pfam database using a parallelized version of the program hmmpfam. The user can perform queries with one or more sequences at a time and then receive the results by e-mail.
website       summary

SLiMDisc
SLiMDisc (Short Linear Motif Discovery) is a tool for finding shared motifs in proteins with a common attribute such as sub-cellular location or a common interaction partner.
website       summary

SLiMFinder
SLiMFinder web server is a de novo motif discovery tool for short linear motifs (SLiMs). Statistically over represented motifs within a set of protein sequences are identified and scored. Users have numerous masking options t...
website       summary

SLiMSearch
Short, Linear Motif Search (SLiMSearch) allows identification of a user defined SLiM in a proteome or set of sequences, using conservation and protein disorder context statistics to rank occurrences.
website       summary

SLITHER
SLITHER is a web server for protein channel studies. It generates contiguous conformations of a molecule along a curved tunnel inside a protein and calculates the ensuing binding free energy profile.
website       summary

SMAP-WS
The SMAP web service provides a user friendly interface and programming API to study protein-ligand interactions. Useful for understanding the structure, function and evolution of proteins and for designing safe therapeutics.
website       summary

SMART
SMART (Simple Modular Architecture Research Tool) is a web tool for the identification and annotation of protein domains, and provides a platform for the comparative study of complex domain architectures in genes and proteins...
website       summary

SMOG@ctbp
SMOG@ctbp is a web server for structure based modeling. It is based on the GROMACS molecular dynamics package and comes with tutorials.
website       summary

SMPDB
The Small Molecule Pathway Database (SMPDB) is an interactive, visual database containing more than 350 small-molecule pathways found in humans. SMPDB is designed specifically to support pathway elucidation and pathway discov...
website       summary

snoGPS
snoGPS allows you to search for H/ACA snoRNA (small nucleolar RNA) genes in a genomic sequence
website       summary

snoscan
Snoscan allows you to search for C/D box methylation guide snoRNA (small nucleolar RNA) genes in a genomic sequence
website       summary

SNOW
SNOW is a web-based tool for the statistical analysis of protein-protein interaction networks. Input is a collection of protein or gene indentifiers onto the interactome scaffold. Output includes statistical significance esti...
website       summary

snowdeal.org > {bio,medical}informatics
A weblog that provides daily updates and links to news items and stories of interest to bioinformatics community.
website       summary

SNPbox
Tool for large-scale standardized primer design with specific modules for SNP and exon PCR amplification. Results are presented as HTML with genomic position, primer sequence, and PCR conditions. Precomputed SNPbox results fo...
website       summary

The SNP Consortium
Non-profit foundation whose mission is to develop up to 300,000 SNPs distributed evenly throughout the human genome and to make this information available to the public without intellectual property restrictions.
website       summary

SNP Cutter
SNP Cutter is a tool that automates PCR-RFLP assay design for SNP genotyping.
website       summary

SNP@Domain
SNP@Domain identifies SNPs within human protein domains allowing users to investigate SNPs in the context of two dimensional and three dimensional maps. Links to external databases (Pfam, SCOP, Ensembl, dbSNP, OMIM, SIFT) are...
website       summary

SNPinfo
A suite of web=based tools for SNP detection. Functional predictions of SNP affect on protein structure, gene regulation, splicing and miRNA binding are incorporated.
website       summary

SNPmasker
SNPmasker masks SNPs in a given sequence using information from the dbSNP database. This tool can also be used to mask repeat sequences. SNPmasker is primarily designed for masking the sequences before primer and probe design...
website       summary

SNPsyn
SNPsyn is a tool for the discovery of synergistic pairs of SNPs from large genome-wide case-control association studies data on complex diseases. The SNPsyn web server receives GWAS data submissions, invokes the interaction a...
website       summary

soaPDB
soaPDB is a web application for the generation and organization of saved PDB searches as well email notifications.
website       summary

SOBA: Sequence Ontology Bioinformatics Analysis
Sequence Ontology Bioinformatics Analysis (SOBA) provides a simple statistical and graphical summary of an annotated genome. To be used by annotators and for genome comparison.
website       summary

Sockeye
Sockeye is a visualization tool allowing one to assemble and analyze genomic information in a three dimensional workspace. It can be used to view features at various levels, ranging from SNPs to karyotypes. Sockeye displays g...
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Software for MacOSX at Mek&Tosj.com
Freely available programs that run on the MacOSX platform. 4Peaks is a DNA sequence editor and visualization program able to read and write common trace file formats. iRNAi assists in the design of error-free oligos. EnzymeX ...
website       summary

Software.ncrna.org
A suite of tools for analyzing non-coding RNA sequences on the basis of their secondary structures. Tools include those for structural multiple sequence alignments, structural pairwise sequence alignments and structural motif...
website       summary

Sol Genomics Network
The Sol Genomics Network (SGN) is a clade-oriented database (COD) containing biological data for species in the Solanaceae and their close relatives, with data types ranging from chromosomes and genes to phenotypes and access...
website       summary

SOURCE
Stanford Online Universal Resource for Clones and ESTs pools publicly available data commonly sought for any clone, GenBank accession, or gene from human, mouse, rat.
website       summary

SoyBase
SoyBase, the soybean genetic database, is a comprehensive repository for curated genetics, genomics and related data resources for soybean. SoyBase contains the most current genetic, physical and genomic sequence maps integra...
website       summary

SPACE
SPACE (Structure Prediction and Analysis based on Complementarity with Environment) is a suite of tools for predicting and analyzing structures of biomolecules and their complexes.
website       summary

Spaced Words
Spaced Words computes alignment-free sequence comparison. Spaced Words uses a pattern of care and don't care positions.
website       summary

SPatt
Statistics for Patterns (SPatt) can compute the significance of a given DNA pattern in a genome sequence. This tool can be used to find patterns with unusual behaviour in DNA sequences.
website       summary

SPEED
Signaling Pathway Enrichment using Experimental Datasets (SPEED) is a web server for enrichment of signaling pathways responsible for gene expression changes.
website       summary

SPIKE
SPIKE (Signaling Pathways Integrated Knowledge Engine) is a database for highly curated interactions for particular human pathways, along with literature-referenced information on the nature of each interaction. Pathways are ...
website       summary

SplicePort
SplicePort makes splice-site predictions for submitted sequences, and allows browsing of the motifs used in the prediction. Feature selection is optimized for human splice sites.
website       summary

SplitPocket
SplitPocket is a web server for identification of functional surfaces of proteins from their structure coordinates. Identification is based on the geometric concept of a split pocket, which is a pocket split by a binding liga...
website       summary

S. pombe genome
Schizosaccharomyces pombe Genome Sequencing Project.
website       summary

SPOT
The SNP Prioritization Online Tool (SPOT) is a web server for integrating biological databases into the prioritization of SNPs for further study after a genome wide association study.
website       summary

SPRING
Sorting Permutation by Reversals and Block Interchanges (SPRING) is a tool for the analysis of genome rearrangements. SPRING takes two or more chromosomes as its input and then computes a minimum series of reversals and/or bl...
website       summary

Spritz
Spritz is a tool for the prediction of disordered regions of proteins.
website       summary

SRA
The Sequence Read Archive (SRA) was established as a public repository for the next-generation sequence data and is operated by the International Nucleotide Sequence Database Collaboration (INSDC). INSDC partners include the ...
website       summary

Sride
Sride is a tool for identificating stabilizing residues in protein structure.
website       summary

SROOGLE
SROOGLE is a webserver that makes splicing signal sequence and scoring data available to the biologist in an integrated, visual and user friendly format.
website       summary

SSA
Signal Search Analysis (SSA) allows for the analysis of nucleic acid sequence motifs that are positionally correlated with a functional site (e.g. a transcription start site).
website       summary

SSEP
Secondary Structural Elements of Proteins (SSEP) provides access to information about secondary structural elements present in non-redundant sets of proteins from the PDB.
website       summary

S-Star.org
Aims to provide a bioinformatics education to interested students everywhere, regardless of background, with the help of the Internet. The lectures are also accessible to the public for those who do not wish to register in th...
website       summary

SStructView
RNA secondary structure viewer applet; must be integrated into web page to be implemented; can link to multiple computational backends.
website       summary

STAMP
STAMP is a tool for exploring DNA-binding motif similarities by providing resources for motif alignment, similarity and database matching.
website       summary

Stanford Microarray Database (SMD)
SMD stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, SMD provides interfaces for data retrieval, analysis and visualization.
website       summary

starBase
StarBase (sRNA target Base) facilitates the comprehensive exploration of miRNA-target interaction maps from CLIP-Seq and Degradome-Seq data. Two web servers are provided to discover novel miRNA target sites from CLIP-Seq and ...
website       summary

STarMir
STarMir is a web server for prediction of microRNA binding sites.
website       summary

Statistics.com
Online statistics courses. Also contains links to statistics software and on-line textbooks.
website       summary

Statistics Notes in the British Medical Journal
Brief descriptions of statistical concepts and methods often combined with clinical/medical examples.
website       summary

StemCellNet
StemCellNet is an interactive platform for network-oriented investigations in stem cell biology. This web-server allows you to interactively query, visualize and interrogate molecular networks in the context of stem cell biol...
website       summary

STING Millenium
STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them.
website       summary

STITCH
STITCH database integrates the data for interactions between small molecules and proteins dispersed over the literature and various databases of biological pathways, drug-target relationships and binding affinities. Interacti...
website       summary

Stitchprofiles.uio.no
Stitchprofiles.uio.no is a server that performs web-based computations on DNA melting. In addition to creating stitch profile diagrams representing the alternative conformations that partly melted DNA can adopt, the server ca...
website       summary

STRAP
The Structural Alignment Program for Proteins (STRAP) is a java-based program that can be run over the web using a Java Web Start enabled browser or downloaded and run as a stand-alone application. Alignments can be done usin...
website       summary

STRIDE
STRIDE takes a PDB structure as input and reports back either secondary structure assignments, a Ramachandran plot or a contact map.
website       summary

STRING
STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) is a protein-protein interaction/association database. Both known and predicted interactions are included. The interactions are derived from existing data s...
website       summary

STRING
STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:Genomic context, High-throughput experime...
website       summary

Struct2Net
Struct2Net is a web server for predicting interactions between arbitrary protein pairs using a structure based approach.
website       summary

StSNP
StSNP (Structure SNP) is a server which provides the ability to analyze and compare human nonsynonymous SNPs (nsSNP) in protein structures, protein complexes, protein-protein interfaces and metabolic networks.
website       summary

SUMOsp
SUMOylation Sites Prediction (SUMOsp) predicts sites for sumoylation, a reversible post-translational modification of proteins by the small ubiquitin-related modifiers (SUMO).
website       summary

SuperCYP
The SuperCYP (Cytochrome P450) database contains about drugs, Cytochrome-Drug interactions and 1,200 alleles. SNPs and mutations are also listed and ordered according to their effect on expression and/or activity. SuperCYP is...
website       summary

SUPERFAMILY
The SUPERFAMILY resource provides protein domain assignments at the structural classification of protein (SCOP) superfamily level for completely sequenced genomes, metagenomes and other gene collections such as UniProt. A new...
website       summary

Superimpose
Superimpose web server performs structural similarity searches for small molecules, parts of proteins (i.e. binding sites) or whole proteins, with a preference towards 3D structure based methods. Users are assisted in selecti...
website       summary

SuperLooper
SuperLooper is a web tool for the modeling of loops in globular and membrane proteins.
website       summary

SuperPose
SuperPose is a tool for superpositions of protein structures. SuperPose generates sequence alignments, structure alignments, PDB coordinates and RMSD statistics, difference distance plots, and images of the superimposed molec...
website       summary

SuperPred
The SuperPred web server compares the structural fingerprint of an input molecule to a database of drugs connected to their drug targets and affected pathways. As the biological effect is well predictable, if the structural s...
website       summary

SuperSweet
SuperSweet is a collection of carbohydrates, artificial sweeteners and other sweet tasting agents like proteins and peptides. Structural information and properties such as number of calories, therapeutic annotations and a swe...
website       summary

SVMHC
SVMHC is a server for prediction of MHC class I and class II binding peptides. SVMHC can be used to find likely binders in a protein sequence and to investigate the effects of single nucleotide polymorphisms on MHC-peptide bi...
website       summary

SVM-PROT
Support Vector Machine of Proteins (SVM-PROT) is a tool for predicting and classifying protein families.
website       summary

SVMtm
Support Vector Machine Transmembrane (SVMtm) predicts transmembrane helices when given protein sequences in FASTA format.
website       summary

SWAKK
Sliding Window Analysis of Ka and Ks (SWAKK) is tool for detecting positive selection in proteins using a sliding window substitution rate analysis. The program can display the results on a 3D protein structure.
website       summary

SWISS-2DPAGE
This is a 2D gel electrophoresis database containing data for proteins identified on SDS-PAGE or 2D-PAGE reference maps.
website       summary

SwissDock
SwissDock is a web server dedicated to the docking of small molecules on target proteins. It is based on the EADock DSS engine.
website       summary

Swiss EMBnet
Swiss EMBnet is a web portal with links and access to various bioinformatics tools and links to institutes that are involved in bioinformatics.
website       summary

Swiss Model
SWISS-MODEL is a fully automated protein structure homology-modelling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make Protein Modelling acce...
website       summary

Swiss-PdbViewer
Excellent tool for comparing, colouring, annotating, mutating 3-D structures; a.k.a. Deep View; tutorial *Molecular Modeling for Beginners* is a must (listed on this page).
website       summary

Swiss-Prot and TrEMBL
Swiss-Prot is a curated database of protein sequences that are highly annotated and have a minimal level of redundancy. TrEMBL is a supplement to Swiss-Prot, containing computer-annotated translations of EMBL sequences.
website       summary

Swiss-Shop
Submit sequence, pattern or keywords to receive email alert when new sequences of interest appear in SwissProt.
website       summary

SwissTargetPrediction
SwissTargetPrediction is a web server for target prediction of bioactive small molecules. This website allows you to predict the targets of a small molecule. Using a combination of 2D and 3D similarity measures, it compares t...
website       summary

SymD
SymD webserver is a platform for detecting internally symmetric protein structures. It works through an “alignment scan” procedure in which a protein structure is aligned to itself after circularly permuting the second co...
website       summary

SymmDock
SymmDock is an server for prediction of complexes with cyclically symmetry by geometry based molecular docking.
website       summary

SynoR
SynoR searches vertebrate genomes for synonymous regulatory elements.
website       summary

Systems Biology Markup Language (SBML)
The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biochemical reaction networks. SBML is applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks...
website       summary

T1DBase
T1DBase is a database for type 1 diabetes (T1D). It integrates genetic, genomic and expression data relevant to T1D research across mouse, rat and human and presents this to the user as a set of web pages and tools. New data ...
website       summary

T3DB
The Toxin and Toxin-Target Database (T3DB) is a unique bioinformatics resource that compiles comprehensive information about common or ubiquitous toxins and their toxin-targets. Each T3DB record (ToxCard) contains over 80 dat...
website       summary

TACT
Transcriptome Auto-annotation Conducting Tool (TACT) is an automated tool for conducting functional annotation of transcripts that integrates sequence similarity searches and functional motif predictions. TACT was originally ...
website       summary

TADB
TADB is an integrated database that provides comprehensive information about Type 2 toxin-antitoxin (TA) loci. TADB offers both predicted and experimentally supported Type 2 TA loci-relevant data. A broad range of similarity ...
website       summary

TarFisDock
Target Fishing Dock (TarFisDock) is a web server that docks small molecules with protein structures in the Potential Drug Target Database (PDTD) in an effort to discover new drug targets.
website       summary

Target Explorer
Target Explorer can be used to create custom matrices to describe transcription factor binding sites (TFBS), search for clusters of TFBS, and identify target genes. Free registration is required.
website       summary

Targetfinder.org
Targetfinder.org provides a web based resource that allows users to find genes that have a similar expression to a query gene signature.
website       summary

TargetRNA
TargetRNA is a web based tool for identifying mRNA targets of small non-coding RNAs in bacterial species.
website       summary

TarO
TarO is a collection of tools for protein target optimization analysis. Tools include those for annotation of putative orthologues and homologues, searches against the PDB with PSIBLAST, generation of annotated multiple seque...
website       summary

Taverna
Taverna is a tool for creating and running bioinformatics workflows.
website       summary

taveRNA
taveRNA hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is an alternative to many RNA folding methods. inteRNA predicts the joint secondary structure of two RNA sequences. pRuNA is an database pruning method...
website       summary

TCAG: The Centre for Applied Genomics, Toronto
The Centre for Applied Genomics is a Canadian centre for human genome and disease research. Resources include Genomic and cDNA library screening (human, mouse, dog, pig) provided free to Canadian academic researchers with a n...
website       summary

TcoF-DB
TcoF is a database that facilitates the exploration of proteins involved in the regulation of transcription in humans by binding to regulatory DNA regions (transcription factors) and proteins involved in the regulation of tra...
website       summary

T-COFFEE
The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequenc...
website       summary

TEAM
TEAM is a web tool for the design and management of panels of genes for targeted enrichment and massive sequencing for clinical applications.
website       summary

text2genome
text2Genome is a hybrid text mining/genome annotation application that extracts DNA sequences from biomedical articles and automatically maps them to genomic databases.
website       summary

TFAM
TFAM is a system to classify the function of tRNAs that is based on tRNA structural alignments.
website       summary

TFBScluster
TFBScluster is a web tool designed to identify clusters of transcription factor binding sites (TFBSs) conserved in mammalian and mouse genomes. By entering a specified range of TFBS, you can retrieve a list of SWISS-PROT char...
website       summary

TFM-Explorer
TFM-Explorer web server is a toolbox for the identification of putative transcription factor binding sites within a set of upstream regulatory sequences for a given set of genes. Only for human, mouse, rat, chicken and drosph...
website       summary

TGGE-STAR
TGGE-STAR assists in the design of PCR primers for temperature gradient gel electrophoresis. It also incorporates the concept of bipolar clamping.
website       summary

THREaD Mapper Studio
THREaD Mapper Studio is a web site that implements a novel, visual and interactive method for the estimation of genetic linkage maps from DNA markers.
website       summary

ThYme
The ThYme (Thioester-active enzYme) database has amino acid sequences and 3D (tertiary) structures of all the enzymes constituting the fatty acid synthesis and polyketide synthesis cycles.
website       summary

TIARA
Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (C...
website       summary

TiCo
TIS Correction (TiCo) is a tool for improving predictions of prokaryotic Translation Initiation Sites (TIS). TiCo can be used to analyze and reannotate predictions obtained by the program GLIMMER.
website       summary

TIGR Gene Indices
An analysis of a set of unique, highly accurate virtual transcripts that are represented in the worlds public EST data; can perform a BLAST search against the TIGR unique Gene Indices.
website       summary

TIGR Software Tools
A list of open-source software packages available for free from The Institute for Genomic Research (TIGR).
website       summary

TMBETA-NET
Tool that predicts transmembrane beta strands in an outer membrane protein from its amino acid sequence.
website       summary

TMH Benchmark
The Transmembrane Helix (TMH) Benchmark server provides a standard benchmark evaluation for helical trans-membrane prediction methods.
website       summary

TMPad
TMPad (TransMembrane Protein Helix-Packing Database) integrates experimentally observed helix-helix interactions and related structural information of membrane proteins. The TMPad offers pre-calculated geometric descriptors a...
website       summary

TMpred
Prediction of transmembrane regions and their orientation.
website       summary

TmPrime
TmPrime allows users to design oligonucleotide sets for gene assembly by both ligase chain reaction and polymerase chain reaction. The program also provides functions to separate long genes into smaller fragments for multi-po...
website       summary

TogoTable
TogoTable TogoTable is a web tool to add user-specified annotations from several biological databases to a user-uploaded table that contains identifiers of a biological database.
website       summary

TogoWS
TogoWS service provides solutions to web service incompatibilities such as interface and data type incompatibilities. TogoWS REST API and TogoWS SOAP API resolve these issues.
website       summary

Tomato Functional Genomics Database
Tomato Functional Genomics Database (TFGD) provides a comprehensive resource to store, query, mine, analyze, visualize and integrate large-scale tomato functional genomics data sets. Computational pipelines have been develope...
website       summary

@TOME-2
@TOME-2 is a web pipeline dedicated to protein structure modeling and small-ligand docking based on comparative analyses. Fold-recognition, template selection, structural alignment editing, structure comparisons, 3D-model bui...
website       summary

TOPCONS
TOPCONS is a web server for consensus prediction of membrane protein topology. Users may constrain parts of the input protein sequence to known inside/outside location.
website       summary

TopMatch
TopMatch is a computational tool for protein structure alignment, for the visualization of structural similarities, and for highlighting relationships found in protein classifications.
website       summary

ToppCluster - comparative enriched features network generator and analyzer
ToppCluster is a human/mammalian genomes-centered web server application for comparative enrichment and network analysis of multiple gene lists. Features such as Gene Ontology terms, protein interactions,disease or disease-as...
website       summary

ToppGene Suite
ToppGene has a suite of tools for gene list functional enrichment, gene prioritization and identification of novel disease genes in an interactome.
website       summary

ToppMiR
ToppMiR web server ranks microRNAs and their mRNA targets based on biological functions and context.
website       summary

TOPSAN
The Open Protein Structure Annotation Network (TOPSAN) is a platform for exploring and annotating structures determined by structural genomics efforts. The TOPSAN platform facilitates collaborative annotation and investigatio...
website       summary

Torque
Torque is a web server for querying of protein-protein interaction networks or pathways across species. Networks of up to 25 proteins may be input.
website       summary

TOUCAN 2
TOUCAN 2 is a regulatory sequence analysis workbench for Metazoan sequences, directly linked with the Ensembl database and implementing SOAP clients for diverse alignment and motif detection algorithms.
website       summary

T-profiler
T-profiler is a tool for the analysis of gene expression data from yeast that uses the t-test to score changes in the average activity of pre-defined groups of genes.
website       summary

TRACTS
TRACTS calculates the frequencies, locations and lengths of all binary tracts (pairs of nucleotide combinations) in DNA sequences. Annotated output will include exon/intron regions and tract information.
website       summary

TraFaC
TraFaC (Transcription Factor Binding Site Comparison) is a tool that identifes regulatory regions using a comparative sequence analysis approach.
website       summary

TRAMPLE
TRAMPLE is a tool for the prediction of transmembrane helices, transmembrane strands, secondary structure, and signal peptides.
website       summary

TRANSFAC
Transcription Factor Database of eukaryotic cis-acting regulatory DNA elements and trans-acting factors; free for non-commercial use.
website       summary

TransFind
TransFind web server predicts transcription factor binding sites in promoter regions of co-regulated gene sets.
website       summary

transFold
transFold predicts the super-secondary structure of transmembrane beta-barrel (TMB) proteins including side-chain orientation and topology of transmembrane segments.
website       summary

TranslatorX
TranslatorX is a web-server designed to align protein coding nucleotide sequences based on their corresponding amino acid translations rather than nucleotide alignments.
website       summary

TransmiR
The TF-miRNA regulatory database (TransmiR) contains transcription factors and miRNAs along with regulatory pairs. References to the published literature (PubMed ID) information about the organism in which the relationship wa...
website       summary

TreeDet
Tree Determinant (TreeDet) is a tool for predicting functional residues in protein sequence alignments.
website       summary

TreeDomViewer
TreeDomViewer is a tool for the visualization of phylogeny and protein domain structure. TreeDomViewer constructs phylogenetic trees and projects the corresponding protein domain information onto the multiple sequence alignme...
website       summary

Tree Editors
Tree Editors is an annotated listing of software for the visualization and manipulation of phylogenetic trees.
website       summary

TreeJuxtaposer
TreeJuxtaposer is a free software tool that allows a visual comparison of two trees in Newick format (phylogenies, taxonomies, gene trees, etc.). It can work with trees having up to 500,000 nodes, and automatically calculates...
website       summary

Tree of Life
Multi-authored project attempting to represent online the entire phylogeny of life on earth.
website       summary

TREE-PUZZLE
Tree-puzzle is a program that constructs phylogenetic trees from sequence alignments using the maximum likelihood method.
website       summary

TreeSAAP
The software program TreeSAAP measures the selective influences on 31 structural and biochemical amino acid properties during clade-genesis, and performs goodness-of-fit and categorical statistical tests.
website       summary

TreeView
Generates nice graphics of trees; reads multiple tree file formats; available for download to Mac or PC.
website       summary

T-Reg Comparator
T-Reg Comparator is a tool for the analysis of transcriptional regulation that allows you to compare a set of position weight matrices (PWM) against the T-Reg database (a collection of PWMs built from Transfac and Jaspar).
website       summary

TRIP
The TRIP (TRansient receptor potential channel-Interacting Protein) Database is a manually curated database that aims to offer comprehensive information on protein-protein interactions (PPIs) of mammalian transient receptor p...
website       summary

TriTrypDB
TriTrypDB is an integrated database providing access to genome-scale datasets for kinetoplastid parasites. TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei a...
website       summary

tRNADB-CE
The tRNA Gene DataBase Curated by Experts "tRNADB-CE" contains tRNA sequences.
website       summary

tRNAscan-SE
tRNAscan-SE allows you to search for tRNA genes in genomic sequence. (site hosted by Lowe Lab at UCSC)
website       summary

TROD
T7 RNAi Oligo Designer (TROD) aids in the design of DNA oligonucleotides for short interfering RNA (siRNA) synthesis with T7 RNA polymerase. It takes an input of a cDNA sequence and outputs a list of DNA oligos for ordering.
website       summary

Tspred
TSpred is a web server for the rational design of temperature-sensitive mutants. Input is a protein sequence or structure.
website       summary

TTD
Therapeutic Target Database (TTD) has been developed to provide information about therapeutic targets and corresponding drugs. TTD includes information about successful, clinical trial and research targets, approved, clinical...
website       summary

Twinscan
Twinscan is a system for predicting gene-structure in eukaryotic genomic sequences. In order to make its predictions, Twinscan combines the information from predicted coding regions and splice sites with conserservation measu...
website       summary

UBC Bioinformatics Center (UBiC)
A world-class centre of excellence for bioinformatics research and training.
website       summary

UCLA Statistical Computing Portal
The Stat Computing Portal is a single search engine that allows you to search over 20,000 pages on statistical computing. The Stat Computing Portal is broken up into smaller portals focused on these statistical packages -- SA...
website       summary

UCMP Phylogeny Wing
"Phylogeny-Diversity of Life Through Time" is an on-line exhibit at the University of California Museum of Paleontology website. There is an introduction to phylogenetics and cladistics, and you can navigate through a very in...
website       summary

UCSC Cancer Genomics Browser
The UCSC Cancer Genomics Browser comprises a suite of web-based tools to integrate, visualize and analyze cancer genomics and clinical data. The browser displays whole-genome views of genome-wide experimental measurements for...
website       summary

UCSC C. briggsae Genome Browser Gateway
Provides a rapid and reliable display of any requested portion of the C. briggsae genome at any scale, together with dozens of aligned annotation tracks.
website       summary

UCSC C. elegans Genome Browser Gateway
Provides a rapid and reliable display of any requested portion of the C. elegans genome at any scale, together with dozens of aligned annotation tracks.
website       summary

UCSC Fruitfly Genome Browser Gateway
Provides a rapid and reliable display of any requested portion of the fruitfly genome at any scale, together with dozens of aligned annotation tracks.
website       summary

UCSC Fugu Genome Browse Gateway
Provides a rapid and reliable display of any requested portion of the Fugu genome at any scale, together with dozens of aligned annotation tracks.
website       summary

UCSC Genome Browser
The University of California, Santa Cruz (UCSC) Genome Browser website provides a large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of ...
website       summary

UCSC Human Genome Browser Gateway
Provides a rapid and reliable display of any requested portion of the human genome at any scale, together with dozens of aligned annotation tracks.
website       summary

UCSC Mouse Genome Browser Gateway
Provides a rapid and reliable display of any requested portion of the mouse genome at any scale, together with dozens of aligned annotation tracks.
website       summary

UCSC Rat Genome Browser Gateway
Provides a rapid and reliable display of any requested portion of the rat genome at any scale, together with dozens of aligned annotation tracks.
website       summary

UCSC SARS Genome Browser Gateway
Provides a rapid and reliable display of any requested portion of the SARS genome at any scale, together with dozens of aligned annotation tracks.
website       summary

UCSF Chimera
UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, traject...
website       summary

UGENE
UGENE is an integrated bioinformatics tool that aims to integrate popular bioinformatics tools and algorithms within a single visual interface that can be easily used by molecular biologists.
website       summary

UKPMC
UK PubMed Central (UKPMC) is a full-text article database that extends the functionality of the original PubMed Central (PMC) repository. Now includes both a UKPMC and PubMed search, as well as access to other records such as...
website       summary

Ulysses
Ulysses is a system to annotate human genes based on gene interactions in model organisms. Data are transferred from amenable species like yeast, fly, and worm through homology, and functional gene annotation is facilitated t...
website       summary

UM-BBD
The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) contains information on compounds, enzymes, reactions and microorganism entries. It includes a Biochemical Periodic Table (UM-BPT) and a rule-based Pat...
website       summary

UM-PPS
The University of Minnesota Pathway Prediction System (UM-PPS) is a web tool that recognizes functional groups in organic compounds that are potential targets of microbial catabolic reactions and predicts transformations of t...
website       summary

Understanding Evolution
A fantastic site for teaching/understanding evolution.
website       summary

UniGene
Non-redundant sets of expressed genes; each UniGene cluster contains sequences, model organism homologs, map and expression information.
website       summary

UniPrime2
The UniPrime2 web server designs large sets of universal primers when provided with a gene reference ID or FASTA sequence. UniPrime2 works by integrating Blastn, T-Coffee, GramAlign and Primer3 into a single software pipeline...
website       summary

UniPROBE
The Universal PBM Resource for Oligonucleotide-Binding Evaluation (UniPROBE) database is a centralized repository of information on the DNA-binding preferences of proteins as determined by universal protein-binding microarray...
website       summary

UniqueProt
UniqueProt creates representative protein sequence sets by eliminating sequence redundancy based on sequence similiarity. This tool needs to be downloaded and run locally on your own machine.
website       summary

Universal Protein Resource (UniProt)
Universal Protein Resource (UniProt) maintains a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessib...
website       summary

UNIX Tutorial for Beginners
Excellent tutorial for unix beginners.
website       summary

Users Guide to the Human Genome
Hands-on tutorial for using genome browsers as web tools for browsing and analyzing data from the Human Genome Project and other sequencing efforts; features UCSC Genome Browser, the NCBI Map Viewer, and the Ensembl Genome Br...
website       summary

UTRdb/UTRsite
UTRdb is a curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs, derived from several sources of primary data. Experimentally validated functional motifs are annotated and also collated as the UTRsite data...
website       summary

VADAR
Volume, Area, Dihedral Angle Reporter (VADAR) is a web server for qualitative evaluation of protein structure data.
website       summary

VanBUG - Vancouver Bioinformatics User Group
Association of researchers, other professionals, and students in the BC Lower Mainland who have an interest in bioinformatics; monthly meetings will be held to present work, ask questions, share tips and tricks.
website       summary

VAP
VAP is a versatile aggregate profiler for efficient genome-wide data representation and discovery. VAP was designed to be used by biologists and bioinformaticians to analyze genomic datasets to generate aggregate or individua...
website       summary

VarioWatch
VarioWatch (formerly GenoWatch) is a disease gene mining browser for association study. VarioWatch annotates both known SNPs and novel variants using information from public domain websites such as NCBI, UniProt, KEGG and GO.
website       summary

VarMod
VarMod is a web server for modelling the functional effects of non-synonymous variants.
website       summary

VAST
Vector Alignment Search Tool for viewing protein structure neighbours.
website       summary

VectorNTI
VectorNTI is an application for integrated for molecular sequence analysis including primer design, virtual cloning, alignments, and sequence assembly. The free license needs to be renewed every year.
website       summary

Vega Annotation Browser
In collaboration with the genome sequencing centres, Vega attempts to present consistent high-quality curation of finished sequence.
website       summary

Vienna RNA Package
Comprises a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
website       summary

Vienna RNA Websuite
Vienna RNA Websuite is a comprehensive collection of tools for folding, design and analysis of RNA sequences. Tools include folding of single and aligned sequences, prediction of RNA-RNA interactions, design of sequences with...
website       summary

Viral Bioinformatics
Viral Bioinformatics provides access to viral genomes and a variety of tools for comparative genomic analyses.
website       summary

ViralORFeome
ViralORFeome 1.0 is a database and management system that provides an integrated set of bioinformatic tools to clone viral ORFs in the Gateway(R) system. ViralORFeome provides a convenient interface to navigate through virus ...
website       summary

ViralZone
ViralZone web resource provides fact sheets on all known virus families/genera with easy access to sequence data. A selection of reference strains (RefStrain) provides annotated standards to circumvent the exponential increas...
website       summary

VirHostnet
Virus-Host Network is a knowledge-base system dedicated to the curation, the integration, the management and the analysis of virus-host molecular (mainly protein-protein) interaction networks as well as their functional annot...
website       summary

Virtual Library--Yeast
Links to yeast resources.
website       summary

Virtual Ribosome
The Virtual Ribosome is a DNA translation tool with a built-in ORF finder that allows the use of alternative start codons, the IUPAC degenerate DNA alphabet, and all translation tables defined by the NCBI taxonomy group. The ...
website       summary

Virus Genotyping Tools
This web server facilitates high-throughput virus genotyping by aligning query sequences to a pre-defined set of reference strains and then computing phylogenetic analysis.
website       summary

VisANT
VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, ...
website       summary

VisCoSe
VisCoSe (Visualization and Comparison of consensus Sequences) is a web based tool that takes a set of sequences (aligned or unaligned) and calculates a consensus sequence and the conservation rates for the sequence alignment,...
website       summary

VisHiC
VisHiC is a web server for clustering and compact visualization of gene expression data combined with automated function enrichment analysis. Output includes a heatmap of the expression matrix highlighting enriched clusters.
website       summary

VISIBIOweb
VISIBIOweb is a web-based pathway visualization and layout service for pathway models in BioPAX format. Models are based on the Systems Biology Graphical Notation and pathway object properties such as external database refere...
website       summary

VISTA
VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or exam...
website       summary

VKCDB
The Voltage-gated K(+) Channel DataBase (VKCDB) contains full-length or nearly full-length unique channel sequences from Bacteria, Archaea and Eukaryotes. Corresponding nucleotide sequences of the open reading frames correspo...
website       summary

VLinux
VLinux is a bootable Linux distribution based on Knoppix. It does not require installation, and contains several bioinformatics software packages including EMBOSS, Phylip, ClustalX, HMMER and Rasmol.
website       summary

VnD
The variations and drugs (VnD) is a consolidated database containing information on diseases, related genes and genetic variations, protein structures and drug information. The VnD database is a useful platform for researcher...
website       summary

VOMBAT
VOMBAT predicts transcription factor binding sites (TFBS) and other motifs in sequence data based on Variable Order Markov models and variable order BAyesian Trees.
website       summary

w3c.org
The world wide web consortium. Keep up to date with new internet standards.
website       summary

WAR
Webserver for Aligning structural RNAs (WAR) is a collection of methods for performing multiple alignments and secondary structure prediction for non-coding RNA sequences. The methods can be run simultaneously and a consensus...
website       summary

WatCut
WatCut allows you to perform restriction analysis and silent mutation analysis. The restriction analysis results can be displayed as a table or graphically to compare the results of different digests. All commercially availab...
website       summary

waviCGH
waviCGH is a web server for the analysis and comparison of genomic copy number alterations in multiple same species samples. For human, mouse and rat genomes, results are mapped back onto the genome.
website       summary

WAViS
The Web Alignment Visualization Server (WAViS) provides various web tools to enhance the presentation of amino acid or nucleotide multiple sequence alignments.
website       summary

WDAC
The WDAC (Weighted Domain Architecture Comparison Tool) is a web-based server to perform protein homology search by comparing protein domain architectures, defined as a sequential order of domains in a protein.
website       summary

Web 3DNA
The web 3DNA server is the web interface for the 3DNA suite of programs developed for the analysis, reconstruction and visualization of 3D nucleic acid containing structures.
website       summary

WebFEATURE
WebFEATURE is a structural analysis tool for identifying 3D physiochemical motifs in molecular structures.
website       summary

WebFR3D
WebFR3D is the online version of Find RNA 3D, a program for annotating atomic-resolution RNA 3D structure files and searching them efficiently to locate RNA 3D structural motifs such as hairpin, internal or junction loops and...
website       summary

WebGestalt
WebGestalt (WEB-based GEne SeT AnaLysis Toolkit) is a system facilitating the analysis of sets of genes. Gene sets can be compared using set operations (intersection, union, etc.), different annotations can be selected and re...
website       summary

WebGeSTer DB
WebGeSTer DB a database of intrinsic transcription terminators identified in bacterial genome sequences and plasmids. Users can obtain both graphic and tabular results on putative terminators based on default or user-defined ...
website       summary

WebGMAP
A web server with a suite of tools for cDNA-genome alignment, visualization and mining. The sequence viewer allows for nucleotide positioning, 6-frame translations, sequence reverse complementation and imperfect motif detecti...
website       summary

WebInterViewer
WebInterViewer is a tool for visualizing molecular interaction networks. It employs a fast-layout algorithm, and can visualize data from interaction databases directly.
website       summary

WebLab
An integrative knowledge sharing system that supports collaboration of biological researchers from various fields. WebLab allows users to fetch, analyze with more than 260 integrated bioinformatic tools, manipulate and share ...
website       summary

WebLogo
WebLogo allows one to create graphical representations (sequence logos) of multiple sequence alignments. This can be done from the website and the source code for WebLogo is also available for download.
website       summary

WebMOTIFS
WebMOTIFS is a tool for motif discovery, scoring, analysis, and visualization. It allows you to use different programs (AlignACE, MDscan, MEME, and Weeder) to search for DNA-sequence motifs, and evaluate the results.
website       summary

webPIPSA
webPIPSA is the web server for Protein Interaction Property Similarity Analysis (PIPSA), a procedure for the comparison and analysis of protein electrostatic potentials for a large number of related protein structures. The re...
website       summary

webPRC
Web Profile Comparer (webPRC) is a web server for searching for distant homologs or similar alignment in domain databases. Results may be provided as either multiple sequence alignments or aligned hidden Markov models. An ali...
website       summary

WebPrInSeS
WebPrInSeS is a web server that allows automated full-length clone sequence identification and verification using high-throughput sequencing data from any of the 3 major sequencing platforms.
website       summary

WebProAnalyst
WebProAnalyst is a tool for searching for residues whose substitutions are correlated with variations in protein activity. Key physicochemical characteristics of these sites can be calculated.
website       summary

WEB-THERMODYN
WEB-THERMODYN analyzes DNA sequences and computes the DNA helical stability. This tool can be used to predict sites of low helical stability present at regulatory regions for transcription and replication.
website       summary

WebTraceMiner
WebTraceMiner is a tool for processing and mining Expressed Sequence Tag (EST) trace files. It can help characterize 3\' and 5\' termini of cDNA inserts by detecting sequence features such as vector fragments, adapt...
website       summary

Web Weeder
Server which identifies conserved motifs within sets of related regulatory DNA sequences, which are likely to be transcription factor binding sites. The interface will automatically conduct several runs using different parame...
website       summary

WEGO
Web Gene Ontology Annotation Plot (WEGO) helps visualize the annotation of sets of genes. WEGO can compare gene annotation datasets by plotting the distribution of gene ontology (GO) annotation results into a histogram.
website       summary

Weighbor
Weighbor is a tool for building phylogenetic trees from distance matrices. It employs a weighted version of the neighbour-joining method in which longer distances in the matrix are given less weight.
website       summary

WhETS
WhETS (Wheat Estimated Transcript Server) is a resource that combines Triticeae ESTs/mRNAs with rice genes to find the best estimate of hexaploid wheat transcript sequences for a target gene, supplemented with information on ...
website       summary

WhichGenes
WhichGenes is a web based tool for gathering, building, storing and exporting gene sets with application to gene set enrichment analysis. The user may export a gene set in any desired output format with multiple gene identifi...
website       summary

Whole Mouse Catalog
Numerous links to Internet resources for mouse and rat research; resource categories include genome, cell, organ, organism, laboratory etc.
website       summary

WikiGene
WikiGene is a scientific project that follows a community-based approach to collect data about genes and gene regulatory events.
website       summary

Wise2
The Wise2 form compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.
website       summary

WIWS
WHAT IF Web Services (WIWS) is a web service based on the WHAT IF software package for macromolecular analysis, visualization, modeling and structure validation. This protein structure bioinformatics web service collection ha...
website       summary

WoLF PSORT
WoLF PSORT is an extension of the PSORT II program for protein subcellular location prediction.
website       summary

Women in Biology Internet Launch Pages
Provides a starting point for biologists who are women; includes information on the history of women in science, education of women scientists, organizations, and careers.
website       summary

WordSpy
WordSpy allows the user to search for over-represented words in a set of sequences and to search for discriminative words using negative sequence data. WordSpy employs this functionality as a means to search for transcription...
website       summary

WormBase
Repository of mapping, sequencing and phenotypic information about C. elegans and C. briggsae.
website       summary

WormBase
WormBase is a data repository for nematode biology. WormBase has expanded to include the complete genomic sequence, gene predictions and orthology assignments from a range of related nematodes.
website       summary

WormNet v3
WormNet v3 is a network-assisted hypothesis-generating web server for Caenorhabditis elegans.
website       summary

Wurst
Wurst is a protein structure prediction tool that uses threading, aligning submitted sequences to thousands of PDB template structures.
website       summary

wwLigCSRre
The wwLigCSRre web server performs ligand-based screening using 3D molecular similarity engine. Inputted 3D ligand molecules may be screened against banks such as Kinase-, CNS-, GPCR-, ion-channel-, antibacterial-, anticancer...
website       summary

XenBase
Xenbase is the model organism database for Xenopus laevis and X. (Silurana) tropicalis. New content has been added including a section on gene expression patterns that incorporates image data from the literature, large scale ...
website       summary

XML Central of DDBJ
XML Central of the DNA Data Bank of Japan (DDBJ) provides SOAP (Simple Object Access Protocol) server and web services for various databases and bioinformatics programs.
website       summary

XplorMed
XplorMed is a tool that summarizes MEDLINE search results according to subjects and allows you to navigate through abstracts in an interactive fashion.
website       summary

xREI
xREI is a web interface that allows users to explore a range of predefined phylo-grammars or create their own phylo-grammar. Grammars are visualized via state transition graphs and substitution matrices. xREI is based on xrat...
website       summary

XTMS
XTMS is a web server for pathway searching in an eXTended Metabolic Space.
website       summary

YASARA
YASARA (Yet Another Scientific Artificial Reality Application) is a software package for visualization, simulation and modeling of molecules. It uses Portable Vector Language (PVL) which allows the visualization of very large...
website       summary

YASS
YASS performs local alignments of DNA sequences. It is available through a web interface and as a standalone command-line tool.
website       summary

Yeast MetaboliNER
Yeast MetaboliNER is a tool to automatically identify metabolite names in the literature, and associate structures where possible, to define the reported yeast metabolome.
website       summary

YEASTRACT
The YEAst Search for Transcriptional Regulators And Consensus Tracking (YEASTRACT) is a curated repository of regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae. YEASTRACT ...
website       summary

Yeast Resource Center
Provides expertise and access through collaboration to mass spectrometry, two-hybrid arrays, deconvolution fluorescence microscopy and protein structure prediction; very good info on each of the techniques.
website       summary

YLoc
YLoc is a web server for the prediction of subcellular localization. Predictions are explained and biological properties used for the prediction highlighted. In addition, a confidence estimates rates the reliability of indivi...
website       summary

YMF 3.0
YMF 3.0 (Yeast Motif Finder) is a tool that identifies good candidates for transcription factor binding sites by searching for statistically overrepresented motifs. Multiple organisms are supported including human, yeast, wor...
website       summary

YOGY
Eukaryotic Orthology (YOGY) is a resource for retrieving orthologous proteins from nine eukaryotic organisms. Using a gene or protein identifier as a query, this database provides comprehensive, combined information on orthol...
website       summary

Yourgenome.org
A resource site from the Wellcome Trust Sanger Institute with information on genomes and the social implications of genomic science. It is organized into three sections based on the background knowledge of the reader.
website       summary

YPA
The Yeast Promoter Atlas (YPA) database collects promoter features in Saccharomyces cerevisiae. YPA integrates nine kinds of promoter features including promoter sequences, genes' transcription boundaries-transcription start ...
website       summary

ZFIN
The Zebrafish Information Network (ZFIN). ZFIN serves as the zebrafish model organism database.
website       summary

ZFIN
ZFIN, the Zebrafish Model Organism Database serves as the central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. ZFIN manually curates comprehensive data for zebrafish gen...
website       summary

ZiFiT
ZiFiT (Zinc Finger Targeter) assists in the design of zinc finger proteins that can bind to specific DNA sequences. ZiFiT has been updated to integrate additional tools and resources including scoring schemes for modular asse...
website       summary

Zinc Finger Tools
Zinc Finger Tools provides several tools for selecting zinc finger protein target sites and for designing the proteins that will target them.
website       summary

zPicture and multi-zPicture
zPicture (pairwise alignment) and multi-zPicture (multiple alignment) are web-based sequence alignment tools based on the blastz alignment program. Alignments from zPicture can be automatically submitted to rVista.
website       summary

The Zuker Group
Algorithms, thermodynamics and databases for RNA secondary structure.
website       summary

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