Oxford Journals | Life Sciences | Nucleic Acids Research

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123 Genomics: Courses, College Degrees and Training
Links to Courses, College Degrees and Training at 123 Genomics - a Genomics, Proteomics and Bioinformatics Knowledge Base
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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-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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3D-Jury
3D-Jury is a protein structure prediction server that collects predictions from multiple servers and generates the final model using a consensus approach.
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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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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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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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ACMES
ACMES (Advanced Content Matching Engine for Sequences) is a server that can be used to search for short repeats (between 3 and 10 000 bases) across multiple species. Users can limit results of a search by keyword searches.
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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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ADVICE
Automated Detection and Validation of Interaction by Co-Evolution (ADVICE) takes a list of protein sequences or sequence pairs as input and uses orthologous sequences to assess the similarity in the evolutionary history of th...
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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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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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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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AISMIG
AISMIG (An Interactive Server-side Molecule Image Generator) is a tool for generating and visualizing high resolution 3D images from PDB structure files.
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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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AliWABA
Alignment on the with an A-Bruijn Approach (AliWABA) is a web based version of a method for multiple sequence alignment that represents an alignment as a directed graph and has proved useful in aligning nucleotide and amino a...
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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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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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AMOD
AMOD (Assisted Morpholino Design) is a tool for designing antisense morpholino oligonucleotides (reagents to modulate gene expression) for an input sequence.
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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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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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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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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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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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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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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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Argonne National Laboratory - Computational Biology Databases
Provides several tools including WIT2, EMP, MPW, SENTRA and PatScan; other tools are also available.
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ArrayExpress
Public repository for microarray based gene expression data; contains several curated gene expression datasets.
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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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ArrayProspector
ArrayProspector is a set of predicted functional associations between genes that have been inferred from microarray expression data from the Standford Microarray Database. Users can search for genes linked to query or for lin...
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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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AS2TS
The AS2TS (Amino acid Sequence to Tertiary Structure) system consists of servers for protein structure analysis and modelling.
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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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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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ASGS
Alternative Splicing Graph Server (ASGS) reads a GFF formatted file for a single gene and creates a splicing graph generated as a directed acyclic graph from the transcript information in the GFF file.
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ASIAN
ASIAN (Automatic System for Inferring a Network) is a server for inferring regulatory networks from gene expression profiles that combines cluster analysis, regression analysis, and graphical Gaussian modeling.
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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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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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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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AUGUSTUS
AUGUSTUS is a eukaryotic gene prediction tool for modeling intron length distribution, and searching for motifs and multiple splice variants. It is particularly effective with larger sequences. It can be run through a web int...
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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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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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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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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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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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BhairPred
BhairPred is a tool for predicting beta-hairpins in protein sequences using a support vector machine.
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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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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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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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BioLinux
A resource for pre-compiled linux RPM files (easy-to-install packages) of popular bioinformatics tools. Tools available for download include Clustal W, EMBOSS, PHYLIP and BLAST.
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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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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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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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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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BIOSMILE
BIOSMILE is a web-based NCBI PubMed search tool. Users input keywords to be searched and BIOSMILE retrieves matching PubMed abstracts.
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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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BIPASS
BioInformatics Pipeline Alternative Splicing Services (BIPASS) provides access to alternative splicing information extracted from various public databases and allows users to submit their own transcript and genome sequences f...
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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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BLAST2SRS
BLAST2SRS (Sequence Retrieval System) is a tool to retrieve protein sequences using similarity (BLAST) and keyword searches.
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BLAST Filter
A tool that uses BLAST analyses to assemble a set of sequences from a single query sequence. Users can customize rules which act to filter out certain sequences from the full set of BLAST results.
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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.
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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.
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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...
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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 of co...
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BoxShade
Printing and shading of multiple alignment files.
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BPROMPT
Bayesian PRediction Of Membrane Protein Topology (BPROMPT) uses a Bayesian Belief Network to combine the results of other membrane protein prediction methods for a protein sequence.
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BRENDA - The Comprehensive Enzyme Information System
Information about reaction and specificity, post-translational modifications, structure, stability, and references to other databases; free for academics.
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BRIGEP
The BRIDGE-based Genome-Transcriptome-Proteome Browser (BRIGEP) comprises three open-source web-based systems: GenDB, ProDB and EMMA. GenDB is a bacterial genome annotation system, ProDB is a storage and analysis system for m...
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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...
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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.
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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 t...
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Build your own arrayer
The MGuide (version 2.0). The Brown Labs complete guide to microarraying for the molecular biologist.
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caBIO Web Services
SOAP interfaces used to access the cancer Bioinformatics Infrastructure Objects(caBIO) funtionality.
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CAMPO
CAMPO is a tool to analyze conserved regions from a multiple sequence alignment
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Canada Bioinformatics People
Principal investigators and group leaders from academia, government labs, and industry with an interest in development of bioinformatics resources in Canada.
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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.
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Canadian Bioinformatics Workshops
Hands-on instruction in the use and development of software tools for genomic and computational biology research.
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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.
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Canadian Society for Systems Biology
The Canadian Society for Systems Biology aims at supporting and developing initiatives that strengthen Systems Biology research in Canada.
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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...
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CanPredict
CanPredict uses a combination of computational methods to predict whether specific sequence changes in a protein are likely to be cancer-associated mutations.
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CAP3 Sequence Assembly Program
Web-based contig assembly.
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CAPweb
CGH array Analysis Platform (CAPweb) is a tool for storing, analyzing and visualizing CGH-array data.
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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...
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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....
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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.
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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...
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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).
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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 ...
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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...
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CATH
Database of automated protein structure classification according to Class (C), Architecture (A), Topology (T) and Homologous superfamily (H).
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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.
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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.
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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.
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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...
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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.
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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...
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Center for Law and Genetics
Contains numerous articles concerning the legal and ethical issues arising from the developments in genetic technology.
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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).
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CEP
CEP (Conformational Epitope Prediction) is a server for the prediction of probable antibody binding sites of protein antigens.
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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...
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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...
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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...
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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 ...
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Chilibot
Chilibot searches the PubMed literature database based on specific relationships between proteins, genes, or keywords. The results are returned as a graph.
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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.
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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.
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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...
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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.
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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...
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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.
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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...
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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.
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cisRED
cisRED is a database system for genome-scale computational discovery of regulatory elements.
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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...
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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.
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ClustalW
Standard multiple sequence alignment.
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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...
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Cluster Buster
Cluster Buster is a tool that finds clusters of pre-specified motifs in DNA sequences.
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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.
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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 ...
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CMS Molecular Biology Resource
Compendium of electronic and Internet-accessible tools and resources for Molecular Biology, Biotechnology, Molecular Evolution, Biochemistry and Biomolecular Modeling.
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Cn3D
Web browser helper application that simultaneously displays 3-D structure, sequence, and alignment.
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CNplot: Visualization of Pre-Clustered networks
CNplot is a network visualization tool that can be used for large-scale networks, as long as they are pre-clustered.
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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...
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CODEHOP
COnsensus-DEgenerate Hybrid Oligonucleotide Primers (CODEHOP); degenerate PCR primer design; will accept unaligned sequences.
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CodonO
CodonO is a method for measuring synonymous codon usage bias within and across genomes.
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Codon Usage Database
Find GC content and frequency of codon usage for any organism that has a sequence in GenBank.
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COFECO
COFECO is a web-based tool for composite annotation of protein complexes, KEGG pathways and Gene Ontology terms for an input class of genes. COFECO provides a GO hierarchical viewer and KEGG pathway viewer for visualizing enr...
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COGs
Clusters of Orthologous Groups represent ancient conserved protein domains; use COGnitor tool to find COGS in sequence of interest.
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COILS
Prediction of coiled coil regions.
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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...
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Color Base Pair
On-line bioinformatics resources including links to news, forums, tutorials, and jobs.
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Combinatorial Extension of the Optimal Path
Calculates structural alignments between two protein chains; or between a single chain and the entire Protein Data Bank.
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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.
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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...
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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...
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ConPred II
ConPred II is a tool for predicting transmembrane topology for a user-supplied query sequence. Results are presented in a variety of forms including hydropathy plots.
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CONREAL
CONREAL (Conserved Regulatory Elements Anchored Alignment) allows identification of transcription factor binding sites (TFBS) that are conserved between two orthologous promoter sequences.
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Consensus Server
The Consensus server aligns a sequence to a structural template using a consensus of 5 different alignment methods. A measure of reliability is produced for each alignment position in order to predict the suitability of regio...
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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...
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Consite
Detect transcription factor binding sites in genomic sequences using phylogenetic footprinting and experimentally-confirmed binding profiles.
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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...
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ConTra
The Conserved Transcription Factor Binding Sites (ConTra) is a promoter alignment analysis tool to identify transcription factor binding sites across species. This web served allows users to interactively visualize transcript...
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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...
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CoPub
Useful in microarray data analysis, 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 diff...
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CorGen
CorGenmeasures long-range correlations in DNA sequences and can generate random sequences with the same (or user-specified) correlation and composition parameters.
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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....
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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.
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CPC
CPC (Coding Potential Calculator) distinguishes protein-coding from non-coding RNAs based on the sequence features of the input transcripts.
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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...
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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.
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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...
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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...
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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.
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CRISPRFinder
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Finder detects this family of direct repeats found in the DNA of many bacteria and archaea.
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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...
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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.
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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).
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CrysTwiV
CrysTwiV (Crystal Twin Variables) is an automated approach for phase extension and refinement in X-ray crystallography; free registration is required for use.
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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.
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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...
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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.
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CVTree
Composition Vector Tree (CVTree) infers phylogenetic relationships between microbial organisms by comparing their proteomes using a composition vector approach.
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CysView
CysView takes as input various annotated formats of protein sequences, and graphically displays cysteine pairing patterns. It also groups proteins with similar disulfide connectivity patterns.
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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...
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CytoSVM
CytoSVM is a Support Vector Machine (SVM) based server that predicts putative cytokine-receptor interactions based on a primary protein sequence. Using this method, results from screening the human and mouse genomes are avail...
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DAhunter
DAhunter is a web server for the identification of homologous proteins by comparison of protein domains. Single domains and domain combinations are scored and used in homology identification.
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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.
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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...
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DATF
The Database of Arabidopsis Transcription Factors (DATF) contains information of more than 1800 known and predicted transcription factors for Arabidopsis.
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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.
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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...
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dbEST
Expressed Sequence Tags database; a division of GenBank containing single-pass cDNA sequence reads
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dbSNP
Repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms; NCBI collaboration with NHGRI.
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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...
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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...
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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.
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Degree Programs in Bioinformatics and Computational Biology
A list of university programs in bioinformatics and computational biology maintained by the ISCB.
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Democracy, Ethics and Genomics
Ethical issues in genomics from Genomics, Ethics, Environment, Economics, Law, and Society (GE3LS).
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DeNovoID
DeNovoID is a tool for protein identification using de novo peptide sequence data from mass spectrometry experiments.
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DePIE
Design Primers for Protein Interaction Experiments (DePIE) is a web-based primer design tool for protein interaction experiments.
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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...
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DEREF
Dragon Estrogen Response Element Finder (DEREF) allows the discovery of transcription factor binding sites (TFBS) in vertebrate genomic sequences.
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DGSF
Dragon Gene Start Finder (DGSF) predicts promoters and transcription start sites (TSS) within CpG islands for mammalian DNA sequences.
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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.
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DIAL
DIAL (Domain Identification Algorithm) is a web server for the automatic identification of structural domains given the three-dimensional coordinates of a protein.
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DIAL
DIAL (dihedral alignment) is a server that provides access to a dynamic programming algorithm for structural alignment of RNA.
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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.
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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.
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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.
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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...
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Dicty WorkBench
Dictyostelium discoideum genome annotation and analysis portal; specialized Dictyostelium sequence and function annotaton database; the following features are available for querying: browse entire list of ORFs, view annotatio...
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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.
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DINAMelt
DINAMelt is a tool for predicting hybridization and folding (secondary structure) of DNA and RNA using equilibrium thermodynamic methods.
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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...
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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...
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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.
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DiscoverySpace
DiscoverySpace is a tool for gene expression analyses and biological discovery.
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DisEMBL
A computational tool for prediction of disordered/unstructured regions within a protein sequence.
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DISULFIND
DISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity given a protein sequence.
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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.
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dnaMATE
dnaMATE calculates a consensus melting temperature (Tm) for any given short DNA sequence (16-30 nts) based on three independent thermodynamic data tables. Stand-alone version available; list of other melting temperature calcu...
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DNA Methylation Database
The database contains information about the occurrence of methylated cytosines in the DNA.
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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).
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DNAtools
DNAtools include predicting DNA curvature; plotting physicochemical, statistical, or locally computed paramaters along DNA sequences; producing a 3-D model of a DNA sequence; searching an intron database.
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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.
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Doelan
Doelan is an tool designed to monitor the quality of DNA microarray production.
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The Dog Genome Project
The dog genome project is a collaborative study aimed at producing a map of all of the chromosomes in dogs, which can be used to map the genes causing disease and those genes controlling morphology and behavior.
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DOMAC
DOMAC is an accurate, protein domain prediction server that integrates homology modeling, domain parsing, and ab initio methods together.
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DOMAINATION
DOMAINATION is a method to identify domains in a protein sequence from similarity searches using PSI-BLAST. The identified domains are used in individual PSI-BLAST searches to improve detection of distant homologous sequences...
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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.
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Dotlet
Dot plot tool with very helpful learn by example interpretations of sample outputs.
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Dotter
Dotter is a dot-matrix program with interactive greyscale rendering for genomic DNA and protein sequence analysis.
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DOUTfinder
Domain Outlier Finder (DOUTfinder) is a tool for facilitating protein domain detection among remotely related protein sequences.
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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.
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DRTF
Database of Rice Transcription Factor (DRTF) is a collection of known and predicted transcription factors from japonica and indica rice genomes.
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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 ...
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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...
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DSHIFT
DSHIFT is a web server for predicting chemical shifts of DNA sequences in random coil form or double helical B-form.
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DSSPcont
DSSPcont automates protein secondary structure prediction from PDB structures to reflect structural variations due to thermal fluctuations.
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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...
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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.
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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 ...
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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...
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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.
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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...
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Eclair
Eclair is a web service that implements the Eclat (EST CLAssification Tool) support vector machine (SVM) approach for the classification of species origin for, primarily, expressed sequence tags (ESTs)
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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. ...
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E.Coli Index
comprehensive guide to information relating to E. coli; home of Echobase: a database of E. coli genes characterized since the completion of the genome
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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 ...
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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.
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EGassembler
EGassembler is a pipeline for clustering and assembling sequence fragments from transcript (EST) data or from shotgun sequencing.
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Electronic PCR
Find sequence-based markers (STSs) and therefore, map location in a DNA sequence of interest; useful for detecting mis-priming events.
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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.
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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...
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EMBOSS
Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.
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eMolecules
eMolecules is a search engine for chemical structures that allows for substructure searching.
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ENDEAVOUR
ENDEAVOUR is a computational approach to prioritizing 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...
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ENDscript
ENDscript is a tool for creating, visualizing, and interpreting multiple sequence alignments overlayed with known structural information.
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enoLOGOS
enoLOGOS creates sequence logos based on a variety of input, including sequence alignments, probability and alignment matrices and energy measurements.
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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...
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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.
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Ensembl Drosophila Genome Browser
Access to the Fly genome through the Ensembl user interface (both for visualisation and data mining).
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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.
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Ensembl Genome Browser
Website, MySQL server and perl API access to software system which produces and maintains automatic annotation on eukaryotic genomes.
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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.
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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.
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Ensembl Mouse Genome Browser
Analysis of finished and draft mouse genomic clone sequences.
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Ensembl Rat Genome Browser
The Rat Genome project is an international collaboration to sequence the genome of the brown rat (Rattus norvegicus).
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Ensembl Zebrafish Genome Browser
This ensembl website features the zebrafish whole genome shotgun assembly sequence.
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EnteriX
EnteriX is a collection of tools for viewing pairwise and multiple alignments for bacterial genome sequences.
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Entrez
NCBI information retrieval system, including GenBank, MMDB (structures), genomes, population sets, OMIM, taxonomy and PubMed.
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Entrez Genomes
List of prominent complete genomes with access to BLAST and precomputed conserved domains and protein homologs in complete genome context.
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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...
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ENZYME - Enzyme nomenclature database
Repository of enzyme nomenclature information; useful selection of cross references to other databases; free for research purposes only.
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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 ...
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Eponine
Eponine is a probabilistic method for detecting transcription start sites (TSS) in mammalian genomic sequence, with good specificity and excellent positional accuracy.
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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...
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E-RNAi
E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in Drosophila and C. elegans; can also be used for the design of enzymatically-digested long dsRNA (esiRNAs) for mammalian cells.
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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...
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ESEfinder
ESEfinder is a web-based resource for identifing putative ESEs (exonic splicing enhancers), cis-acting motifs responsible for enhancing splicing.
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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.
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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.
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ESPript
Easy Sequencing in Postscript (ESPript) is a utility which provides postscript output for aligned sequences with graphical enhancements and structural information.
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ESTExplorer
ESTExplorer is an automated suite of programs to pre-process, assemble and functionally annotate ESTs at both DNA and protein level.
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ESTpass
ESTpass is a server for processing and annotating sequence data from expressed sequence tag (EST) projects.
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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...
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Ethical, Legal, and Social Issues - Genome Research
Addresses a variety of ethical issues including genetic testing, gene therapy, privacy and patenting.
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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...
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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.
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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.
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Eureka Alert
Daily news updates on science, medicine, health, and technology.
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The European Bioinformatics Institute (EBI)
The EBI is a centre for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures. The EBI web page is a portal to vari...
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EVA
EValuation of Automatic protein structure prediction; provides a continuous, automated, statistical analysis of structure prediction servers.
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EVAcon
EVAcon automates the continuous evaluation of inter-residue contact prediction servers. Results can be viewed statically or dynamically generated.
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EVALLER
EVALLER predicts potential protein allergenicity from primary amino acid sequence.
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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.
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ExPASy Molecular Biology Server
Expert Protein Analysis System; programs and databases for the analysis of protein sequences, structures and 2-D PAGE.
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ExPASy Proteomics tools
Various tools for protein identification and characterization, similarity searches, pattern and profile searches, post-translational modification prediction, and more.
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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.
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ExpressYourself
ExpressYourself is a web-based platform to process microarray data. It includes tools for background correction, normalization, data processing and filtering.
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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 list of...
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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...
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FAN
FAN (Fingerprint Analysis of Nucleotide sequences) searches nucleotide sequences against the PRINTS database, a collection of protein fingerprints used to assign uncharacterized sequences to known families and hence to infer ...
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FANTOM - Functional Annotation of Mouse
Functional annotations for RIKEN full-length cDNA clones.
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FASTA Programs
Sequence retrieval and comparison tools.
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FastContact
FastContact is a free energy scoring tool for protein-protein complex structures.
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FASTR3D
FASTR3D is a web based search tool that allows users to search the PDB database for structurally similar RNAs from input queries of PDB coordinates for an RNA molecule, an RNA secondary structure or RNA primary sequence.
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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.
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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.
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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 ...
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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...
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FeatureExtract
The FeatureExtract server extracts sequence and feature annotations, such as intron/exon structure, from GenBank entries and other GenBank format files.
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FeatureMap3D
FeatureMap3D is a tool to map protein features and sequence conservation onto homologous structures in PDB.
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FeatureScan
FeatureScan searches for sequence similarity by comparing physico-chemical properties of DNA such as charge, melting enthalpy, conformational parameters, etc.
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FFAS03
The Fold & Function Assignment System (FFAS03) 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.
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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...
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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...
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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).
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FIE2.0
5' end Information Extraction v2 (FIE2) identifies and extracts nucleotide sequence around the promoter region of genes and their translation initiation sites (TIS). User can search by gene/protein name or Locus ID.
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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...
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firestar
Firestar predicts functionally important residues, such as ligand binding sites, using structural templates and alignment reliability.
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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.
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FISH
Family Identification with Structure Anchored HMMs (FISH) is a server for the identification of remote sequence homologues on the basis of protein domains.
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FluGenome
FluGenome is a tool for determining lineages and genotypes of influenza A viruses.
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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.
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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.
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FOLDALIGN
FOLDALIGN is an algorithm for local simultaneous folding and aligning two or more RNA sequences.
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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...
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FOLDOC - Computing Dictionary
FOLDOC (Free Online Dictionary of Computing) is a good place to look up meanings of computer jargon.
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FOLD-RATE
FOLD-RATE predicts the folding rates of proteins from their amino acid sequences.
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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.
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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.
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FootPrinter
FootPrinter is a program for phylogenetic footprinting that identifies regions of DNA that are well conserved across a set of orthologous sequences in order to infer phylogenetic relationships.
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FootPrinter3
FootPrinter3 is a web server for predicting transcription factor binding sites (TFBS) by using phylogenetic footprinting. FootPrinter3 extends the motif discovery algorithms of FootPrinter by making use of local multiple sequ...
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FPC
FPC is a tool to assemble contigs from a set of clones and their restriction fragments.
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Fragnostic
Fragnostic is a tool for exploring common structural elements, or fragments, between proteins which have different folds.
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FRalanyzer
FRalanyzer (Fold Recognition alignment analyzer) takes as input a sequence-structure alignment, automatically searches annotated databases, and highlights the functionally important positions that are identical in the alignme...
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FrameD
FrameD is a program that predicts coding regions in prokaryotic and eukaryotic sequences that may contain frameshifts.
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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).
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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.
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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...
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GBA Server
The GBA Server is an EST-based gene expression profiling and analysis platform. It implements the GBA (Guilt-by-Association) algorithm and, given a UniGene cluster, can be used to find genes with similar expression patterns.
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GC-Profile
GC-Profile is a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences.
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GCUA: Graphical Codon Usage Analyser
Graphical representation of codon bias
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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.
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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 ...
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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...
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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...
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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...
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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.
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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.
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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...
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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...
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GeneAlign
GeneAlign is a gene prediction tool that uses conservation of gene structures and sequence homologies between protein coding regions to increase prediction accuracy. GeneAlign is currently configured to align human and mouse ...
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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.
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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...
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GeneCodis
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...
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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.
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GeneDoc
Multiple sequence alignment editor, analyser and shading utility for Windows.
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GeneExpress2.1
Integrated system for data analysis with information about expression and gene networks, also contains transcriptional regulatory regions database (TRRD).
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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...
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Genefisher
Interactive primer design tool for standard or degenerate primers; will accept unaligned sequences.
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GeneFizz
GeneFizz is a tool for identifying genes using by using the physical characteristics of helix-to-coil transitions in DNA.
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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.
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GeneMark
The GeneMark family of programs employ Markov models and are specifically tuned for gene prediction for sequences from prokaryotes, viral genomes and eukaryotes.
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GeneMatcher
The GeneMatcher is a computer specialized for executing calculation intensive methods in bioinformatics. It has 6912 specialized data processors which allow otherwise computationally prohibitive searches to be run quickly in ...
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Gene Ontology (GO) Consortium
Organized, controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products in many organisms.
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GenePath
GenePath is a tool for automated construction of genetic networks and proposal of genetic experiments from mutant data.
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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.
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GenePublisher
GenePublisher performs automatic normalization, statistical analysis, and visualization of DNA microarray data.
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Gene Regulation
Access to databases, programs and papers related to gene regulation.
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GeneSeeker
GeneSeeker allows you to generate a list of candidate genes related to a human genetic disorder by searching against localization and expression databases.
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GeneSeqer
GeneSeqer is a method to identify exon/intron structure by splice site prediction and spliced alignment in plant genomes.
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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.
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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...
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GeneSilico
GeneSilico is a protein structure prediction meta-server that gives access to various fold-recognition servers.
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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...
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GeneTests
GeneTests is a medical genetics information resource developed for physicians, other healthcare providers, and researchers, available at no cost to all interested persons
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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.
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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...
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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.
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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.
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Geno2pheno
Geno2pheno takes as input an HIV-1 pol-gene DNA sequence and estimates phenotypic drug resistance to 17 antiretroviral drugs.
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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...
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Genome Biology
Research news from the life sciences.
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Genome Biology Release 3 of the Drosophila genome
A series of refereed research articles describing Release 3 of the Drosophila genome are freely available online. The articles describe the finishing and annotation of the genome sequence, computational tools, and functional ...
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Genome British Columbia's Learning Centre
Aimed to keep the general public informed about the science, technology and issues connected with genomics and proteomics.
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Genome Canada
The primary funding resource relating to genomics and proteomics in Canada.
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Genome Centres and Databases
Genome centers and databases listed by organism.
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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.
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Genome Hub
Lists of genome-related sites maintained by the NHGRI on behalf of the International Human Genome Sequencing Consortium.
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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,...
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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).
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GenomeScan
Incorporates protein similarity information when predicting genes; based in part on GENSCAN.
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Genome Sciences Centre, Vancouver
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.
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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.
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Genome Web
News reports on the business and technology of genomics, updated continuously throughout the business day.
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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...
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GenoWatch
A disease gene mining browser for association study. GenoWatch is a real-time batch SNP and short tandem repeat polymorphism pipeline that extracts current information from public domain websites such as NCBI, UniProt, KEGG a...
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GENSCAN
Identification of complete gene structures in genomic DNA.
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GENSTYLE
GENSTYLE is based on the genomic signature paradigm and allows the user to classify and characterize nucleotide sequences using oligonucleotide frequencies.
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GEO - Gene Expression Omnibus
Gene expression and hybridization array data repository; online resource for retrieval of gene expression data from any organism or artificial source.
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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...
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GEPS
Gene Expression Pattern Scanner (GEPS) is a tool for the analysis of patterns of expression in microarray data. Users can upload custom data, or can use this tool to search public data sets from GEO or GNF SymAtlas.
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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...
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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...
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GFS
Genome-based Fingerprint Scanning (GFS) takes as input an experimentally obtained peptide mass fingerprint, scans a genome sequence of interest, and outputs the most likely regions of the genome from which the mass fingerprin...
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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).
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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.
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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...
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GlobPlot
GlobPlot has the ability to plot the tendency towards globularity for a given protein sequence. Can also perform SMART/Pfam domain prediction.
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Glossary of Genetic Terms, NHGRI
Includes audio explanations of terms by researchers in the relevant field of study; Francis Collins explains shotgun sequencing.
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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...
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GlycoFragment
GlycoFragment is a tool that takes the sequence of a carbohydrate structure as input, and calculates all theoretically possible fragments which are likely to occur in mass spectra.
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GlycoSearchMS
GlycoSearchMS takes a list of mass spectra peak values as input and searches for matches with the calculated fragments of SweetDB structures.
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GlyNest and CASPER
GlyNest and CASPER are two independent services, available through this common interface, for predicting NMR spectra given a glycan chemical structure.
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Glyprot
Glyprot is a tool for predicting and modelling all potential N-glycosylation sites in a given 3D structure.
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GNN's Genomics Glossary
A glossary of Genomics-related terms from the Genome News Network.
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GOAL
Gene Ontology Automated Lexicon (GOAL) is a tool for the functional analysis of data from SAGE and microarray experiments. Gene Ontology terms are used as the basis for statistical analysis.
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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...
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Godzilla
The Berkeley Genome Pipeline a.k.a. Godzilla, provides precomputed VISTA plots of sequence conservation between pairs of human, mouse or rat genomes.
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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...
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GoGene
GoGene performs high-throughput text mining to complement annotation of genes. GoGene supports search for genes in PubMed, EntrezGene and BLAST.
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GOLD: Genomes Online Database
Up-to-date list of complete and ongoing genome projects.
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GoPubMed
GoPubMed is a tool that allows users to explore the results of PubMed queries in the context of Gene Ontology (GO) terms.
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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...
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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.
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GPCRsclass
GPCRsclass is a tool for predicting amine-binding receptors based on a protein sequence provided by the user.
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GPRM
Genetic Programming for RNA Motifs (GPRM) finds common secondary structure elements in a set of unaligned RNA sequences.
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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...
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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.
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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...
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GraBCas
GraBCas is a tool for predicting granzyme B and caspase cleavage sites.
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Grail
Grail is a suite of tools which recognizes sequence features like promoters, exon candidates, simple repeats and complex repetitive elements. It also models genes based on the exon candidates.
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GRAMM-X
GRAMM-X is a protein docking server.
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GraphAlign
Provides graphical representations of ClustalW global pairwise alignments for query and subject sequences from BLAST type searches. Graphical representation provides information on high quality sections of the global alignmen...
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GraphWeb
GraphWeb is a web server for biological network analysis and module design using a graphical interface.
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Great Experiments
Short essays explaining classic experiments of the 20th century; most are written by one of the people who actually performed the experiments; free with registration.
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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...
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GridGrinder
Software for microarray image analysis.
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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.
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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.
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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.
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H++
H++ is a tool for the prediction of protonation states and pK of ionizable groups in macromolecular structures.
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Harmony
Harmony is a server to assess the compatibility of an amino acid sequence with a proposed three-dimensional structure.
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Harvester
Harvester provides fast access to public bioinformatic databases and servers for human proteins. Results are returned as a single HTML page that contains the cached and cross-linked output from the following databases/servers...
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HGMP-RC Fugu Genome Project
Comparative mapping and sequencing to facilitate human genome annotation.
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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...
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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...
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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...
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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...
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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).
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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...
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H-Invitational Database
The H-Invitational Database (H-InvDB) is a human gene database containing over 20,000 cDNA clusters from multiple high-throughput cDNA sequencing projects. The website provides a genome browser, blast searching, and searching...
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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...
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HMMER
HMMER is an implementation of profile HMM methods for sensitive database searches using multiple sequence alignments as queries.
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HMMgene
Prediction of vertebrate and C. elegans genes.
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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...
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HOMCOS
Homology Modeling of Complex Structure (HOMCOS) predicts the interacting protein pairs and interacting sites by homology modeling of complex structures. Three services are provided: modeling heterodimers, modeling homodimers,...
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HomozygosityMapper
A web base approach to homozygosity mapping. Users upload SNP genotype files into a marker database for analysis and detection of long homozygous stretches.
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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.
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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...
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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.
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Hubba
Hub Objects Analyzer or Hubba is a web-based service for characterizing nodes of importance within a protein interactome data set.
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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.
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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...
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Human BAC Ends
TIGR BAC end sequencing project; query genomic sequence or clone name against database of BAC end sequences to find set of minimally overlapping clones; these sequences provide highly specific markers.
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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.
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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...
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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...
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HumGen
Access to a comprehensive international database on the legal, social and ethical aspects of human genetics.
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HUPO Proteomics Standards Initiative
HUPO Proteomics Standards Initiative (PSI) provides data representation standards to facilitate the exchange, comparison and validation of proteomics data.
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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.
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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...
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IBM Genome Annotation Page
IBM's Bio-Dictionary-based Annotations Of Completed Genomes page lists annotations for over 75 complete genomes (archae, bacteria, eurkaryotes, and viruses). You can query these annotations at the sequence level as well as se...
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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.
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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...
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iCE - internet Contig Explorer
Viewer for physical map data (for mouse, rat, cow, Cryptococcus); developed at the Genome Sciences Centre, Vancouver.
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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...
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iCODEHOP
iCODEHOP is an interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide Primers for multiple alignment of protein sequences.
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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...
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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.
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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...
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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...
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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.
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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 ...
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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...
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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 ...
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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...
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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...
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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 ...
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iMolTalk
iMolTalk is a set of tools for protein structure analysis. Users have access to tools to extract information from PDB files, create Ramachandran plots or alpha-carbon distance matrices, align two structures or a sequence to a...
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iMOT
iMOT (interacting MOTif) server is designed to search for spatially interacting motifs among proteins sharing similar 3-dimensional structures.
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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.
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INCLUSive
INCLUSive is a set of tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.
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INDELSCAN
INDELSCAN is a tool for genome-wide identification of indels.
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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...
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INFO-RNA
INFO-RNA is a server for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.
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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.
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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).
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Institute of Enzymology Servers
A set of severs developed by the Institute of Enzymology that includes tools for transmembrane protein structure prediction and structural analyses.
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Integrated Microbial Genomes (IMG)
The Integrated Microbial Genomes (IMG) system facilitates the comparison of genomes sequenced by the Joint Genome Institute (JGI). It can be searched using keywords or BLASTp, and the gene records diplayed include biochemical...
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IntEnz: Integrated relational Enzyme database
The goal of IntEnz is to create a single relational database containing enzyme data from three different sources: the official version of the Enzyme Nomenclature comprising recommendations of the Nomenclature Committee of the...
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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...
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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...
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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.
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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.
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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.
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InterPro
Integrated database of commonly used signature databases (e.g. PROSITE, PRINTS, SMART, Pfam, ProDom); text- and sequence-based searches.
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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...
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InterWeaver
InterWeaver is a tool employing two approaches to detect potential protein interactions by searching for and interpreting evidence available from on-line databases. The first approach finds homologues for a sequence and searc...
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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 ...
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iPDA
iPDA (Integrated Protein Disorder Analyzer) predicts disordered regions of a query protein sequence.
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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.
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iRefIndex
iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index allows the user to search for a pr...
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ISACGH
ISACGH (In Silico Array CGH) is a tool for visualizing array CGH data and/or expression arrays onto chromosomal coordinates to allow for correlations between copy number and gene expression to be observed. ISACGH is included ...
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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.
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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...
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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 ...
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IsoFinder
IsoFinder is a tool for the prediction of isochores for a user-supplied sequence.
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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...
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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...
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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.
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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...
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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 ...
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JAFA
Joined Assembly of Function Annotations (JAFA) queries multiple functional annotation servers including GOblet, GOfigure, GOtcha, and InterProScan to return the gene ontology (GO) terms that are associated with your protein s...
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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.
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java.sun.com
The source for java technology.
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The Java Tutorial
The place to go for your first cup of Java.
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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.
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JEvTrace
Jevtrace is a tool that combines multiple sequence alignments, phylogenetic, and structural data for identification of functional sites in proteins.
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Joes Site - Phylogeny Programs
Comprehensive list of phylogeny packages, compiled by Joe Felsenstein, creator of Phylip.
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JOY
JOY is a program for displaying 3D structural information in a multiple sequence alignment.
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JPD
Java Protein Dossier (JPD) is part of the STING Suite of web based programs for visualization and analyses of molecular structures. JPD can display many different physicochemical parameters for PDB files as well as for struct...
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jpHMM
Jumping Profile Hidden Markov Model (jpHMM) takes a HIV-1 genome sequence and uses a pre-calculated multiple alignment of the major HIV-1 subtypes to predict the phylogenetic breakpoints and HIV subtype of the submitted seque...
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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 ...
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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...
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JProGO
JProGO is a tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information.
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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.
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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.
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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...
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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...
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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...
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KCaM
The KEGG Carbohydrate Matcher (KCaM) takes glycan structures as input and returns a list of similar glycan structures using a tree-structure alignment algorithm.
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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...
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KemaDom
Kernal Machine for Domain Prediction (KemaDom) can predict the number of domains in a protein sequence using the local context information of neighboring amino acids.
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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...
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KinasePhos
KinasePhos is a tool for identifying kinase-specific phosphorylation sites in protein sequences.
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KinasePhos 2.0
KinasePhos 2.0 is a new version of a kinase-specific phosphorylation site prediction tool.
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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).
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Kinefold
Kinefold calculates (and animates) the folding kinetics of RNA sequences including pseudoknots.
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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...
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KNOTS
KNOTS is a web server that detects knots in protein structures.
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KOBAS
KEGG Orthology-Based Annotation System (KOBAS) annotates sequences with KEGG Orthology terms and identifies the frequently occuring (or significantly enriched) pathways among the queried sequences compared against a backgroun...
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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...
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Learn how to use NCBI resources
Seven interrelated modules expose the user to tools and databases currently used by researchers in molecular biology.
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LGA
Local-Global Alignment (LGA) performs structural alignments for two proteins structures or fragments of 3D protein structures.
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Life Science Directory
Extensive list of links to biology resources; compiled by Amos Bairoch of SWISS-PROT.
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LINKER
LINKER is a tool for designing linker peptide sequences for use in the construction of fusion proteins. The user provides the desired length of the linker in either Angstroms or number of residues, and several other constrain...
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Links to the Genetic World
Large directory of online resources.
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Linux.com
This site has great tutorials and links to other linux sites, supported by the OSDN.
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The Linux Cookbook
Tips and techniques for everyday use.
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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.
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Linux Documentation Project
The Linux Documentation Project is a repository of Linux documentation including documents about individual software, HOWTO documents, FAQs, and more.
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Linux Online
Comprehensive information and resources about the Linux Operating System.
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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.
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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.
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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...
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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, ...
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LNAtools
LNAtools is a collection of tools for the design of LNA (locked nucleic acid) substituted oligonucleotides including: melting temperature (Tm) analysis; secondary structure prediction; and probe design for expression arrays, ...
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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.
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Localizome
Localizome predicts transmembrane (TM) helix number and topology for eukaryotic proteins using protein domain information.
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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...
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LOCATE
LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of mouse proteins.
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LOCSVMpsi
LOCSVMpsi is a tool for prediction of eukaryotic protein subcellular localization based on support vector machines (SVM) and PSI-BLAST.
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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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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.
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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...
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LTR_Finder
LTR_Finder (Long Terminal Repeat Finder) is an efficient program for finding full-length LTR retrotransposons in genome sequences.
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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.
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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 mR...
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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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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...
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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.
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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...
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Maize Genetics and Genomics Database
A central repository for public maize information.
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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.
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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...
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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.
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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...
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MASCOT (Matrix Science)
Protein identification by peptide mass; excellent documentation; incorporates code from MOWSE but allows more search methods on more sequence databases.
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MaskerAid
MaskerAid is an enhancement to RepeatMasker which can effect about a 30-fold increase in the speed of RepeatMasker while maintaining sensitivity.
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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.
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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.
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massXpert
massXpert is a proteomics-oriented program mainly concerned with protein physico-chemistry and protein/peptide mass spectra simulations.
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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.
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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.
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MatInspector
Search for potential transcription factor binding sites in your own sequences using TRANSFAC matrices; free for non-commercial use.
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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.
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Mauve
Mauve is a stand-alone software tool for constructing multiple genome alignments.
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MAVID
MAVID performs multiple sequence alignments for large sequences, constructs phylogenetic trees and displays VISTA plots of conserved regions.
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MAVL/StickWRLD
The Multiple Alignment Variation Linker (MAVL) examines a pre-aligned set of nucleotide or protein sequences and detects positive and negative interpositional correlations. The results can then be viewed as a StickWRLD repres...
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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...
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McGill Centre for Bioinformatics
The Centre for Bioinformatics at McGill is committed to developing the area as a focus of academic research excellence.
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McPromoter
The Markov Chain Promoter Prediction Server (McPromoter) uses statistics to predict eukaryotic DNA transcription start sites.
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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.
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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.
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MedKit
MedKit is a helper application for text-mining the MEDLINE abstract database that allows allows random sampling of abstracts and downloads of >10,000 MEDLINE abstracts in XML form. Java modules (query, sample, fetch, and pars...
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MedlineRanker
The MedlineRanker web server allows a flexible ranking of Medline for a topic of interest without expert knowledge.
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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....
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MEDock
MEDock (Maximum-Entropy based Docking) is a tool for predicting ligand binding sites.
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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...
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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...
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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...
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MeMo
Methylation Modification Prediction Server (MeMo) is a server that predicts arginine and lysine sites that undergo methylation using a support vector machine (SVM).
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The Mendel Site
The Mendel Site contains a collection of tools for predicting lipid postranslational modifications and localization signals in protein sequences.
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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...
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MetaboAnalyst
MetaboAnalyst is a web server for metabolic data analysis. Users input a choice of data (NMR peaks, binned spectra, MS peaks, etc) for data processing, normalization, multivariate statistical analysis, graphing, metabolite id...
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Metabolic PathFinding
The Metabolic PathFinding website takes a source and a target metabolic node as input and finds the shortest path between them in a graph based on the reactions and compounds from the KEGG LIGAND database. Various types of in...
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Meta-MEME
Creates hidden Markov model of motif from MEME output and searches sequence database for matches to this motif.
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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...
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metaSHARK
Metabolic Search And Reconstruction Kit (metaSHARK) provides an interactive visualisation platform for the KEGG metabolic network in the form of the SHARKview applet.
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Mfold
Predict RNA secondary structure from sequence; does not predict pseudoknots - see PKNOTS.
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MGAlignIt
mRNA to Genome Alignments (MgAlignIt) aligns mRNA/EST to genome sequences and visualizes the alignment to provides intron/exon structure information.
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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.
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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...
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MHCPred
Major Histocompatibility Complex Predictor (MHCPred) predicts the binding affinities of major histocompatibility complexes to ligands.
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MIAMExpress
MIAME (minimum information about a microarray experiment) compliant microarray data submission tool.
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MICheck
MICheck (Microbial Genome Checker) allows the user to verify gene annotations in previously published microbial genomes.
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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.
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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...
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Microbial Genome Database
MBGD is a database for comparative analysis of completely sequenced microbial genomes using orthologue identification, paralogue clustering, motif analysis and gene order comparison.
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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.
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MicroFootPrinter
MicroFootPrinter identifies the conserved motifs in regulatory regions of prokaryotic genomes using the phylogenetic footprinting program FootPrinter.
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MicroInspector
MicroInspector is a tool that detects miRNA (microRNA) binding sites in your input sequence by searching against databases of known miRNA binding sites.
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MIDAW
MIDAW (MIcroarray Data Analysis Web tool) is a data normalization and analysis tool for microarray data.
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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...
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MinActionPath
MinActionPath calculates the most-probable trajectory between two known structural states of a protein.
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MINER
MINER is a tool for the identification and visualization of phylogenetic motifs (regions within a multiple sequence alignment (MSA) that conserve the overall phylogeny of the complete family).
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MINT - a Molecular INTeractions database
Curated database with a focus on experimentally verified molecular interaction data collected from scientific literature. Emphasis on mammalian organisms.
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miPred
miPred (microRNA Predictor) can distinguish between real and pseudo microRNA precursors.
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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, ...
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miRanalyzer
miRabakyzer is a web server tool for the analysis of deep sequencing experiments for small RNAs. Users input a list of unique reads and copy number. The tool detects all known microRNA sequences annotated in miRBase, finds pe...
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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.
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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.
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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 Scie...
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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...
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MKT
Standard and Generalized McDonald-Kreitman Test (MKT) is a web tool for the molecular level detection of signatures of natural selection.
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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...
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MMDB
Molecular Modelling Database of 3-D structures; experimentally determined structures only.
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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).
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MobilomeFINDER
MobilomeFINDER (Mobile Genome FINDER) is a tool for high-throughput genomic island discovery.
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Modeller
Homology or comparative modeling of 3D protein structures.
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ModelTest Sever
ModelTest is program for the selection the model of DNA evolution (nucleotide substitution) that best fits your data from phylogenetic analyses.
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MODi
Modi is a tool that facilitates the interpretation of tandem mass spectra in order to identify post-translational modifications (PTMs) in a peptide.
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MODPROPEP
MODPROPEP is a server for structural modeling of protein kinases and MHC proteins in complex with their substrate peptides.
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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 ...
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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...
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Molecular Modeling for Beginners
Excellent hands-on Swiss-PdbViewer/Deep View tutorial; a must-do before attempting to use Swiss-PdbViewer.
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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.
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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.
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MOLPROBITY
MOLPROBITY is a structure validation program that can calculate and display steric, H-bonding, and van der Waals interactions for 3D structures of proteins, nucleic acids, and complexes.
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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.
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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 ...
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Montreal Proteomics Network (RPMPN)
A network of researchers working towards the identification, characterization and localization of every protein for every mammalian cell organelle.
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Motif3D
Motif3D is a protein structure viewer for visualizing sequence motifs contained in the PRINTS database on 3D structures.
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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.
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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.
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Mouse BAC Ends
TIGR BAC end sequencing project; query genomic sequence or clone name against database of BAC end sequences to find set of minimally overlapping clones; BACs are same as those fingerprinted by Genome Sciences Centre, Vancouve...
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Mouse BAC Physical Map
BAC fingerprint map of the mouse genome, completed by Genome Sciences Centre, Vancouver.
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Mouse Genetics: Concepts and Applications
Online version of textbook by Lee Silver.
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Mouse Genome Informatics
Integrated access to data on mouse genetics, genomics and biology; Jackson Labs.
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Mouse Resources
Linked list of major mouse genome and mutation resources; maintained by the Trans-NIH Mouse Initiative.
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The Mouse SNP Database
Free access to a database developed by Roche.
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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.
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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...
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MPSRCH
Uses the Smith-Waterman algorithm; runs at BLAST-like speeds without losing sensitivity.
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mreps
mreps is a tool for identifing tandemn repeats in DNA sequences.
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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...
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MSCAN
MSCAN takes as input one or more DNA sequences and a set of transcription factor binding site profiles. It then detects clusters of the binding sites in the sequences.
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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...
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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...
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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.
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MULTIPRED
MULTIPRED is a tool for mapping T-cell epitopes by prediction peptides that bind to human leukocyte antigen (HLA) class I A2, A3 and class II DR supertypes.
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Multi-Q
Multi-Q provides an automated data analysis tool for multiplexed protein quantitation based on iTRAQ labeling.
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MuPlex
Multi-Objective Multiplex PCR Assay Design (MuPlex) is a tool to assist in the design of multiplex PCR assays. MuPlex takes a set of DNA sequences and other experimental information as input and provides a set of multiplex PC...
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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...
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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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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.
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NAST
Nearest Alignment Space Termination (NAST) is a multiple sequence alignment server for comparative analysis of 16S rRNA gene sequences from bacteria and archaea.
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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.
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Nature's Genome Gateway
A comprehensive web resource devoted to genomics. Sections include papers, news, the human-genome, and post-genomics.
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NCBI Assembly Archive
The NCBI Assembly Archive links publically available assembly information with the NCBI Trace Archive's raw sequence data.
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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.
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NCBI Clone Registry
A database that integrates information about genomic clones and libraries, including sequence data, genomic position, and distributor information.
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NCBI C++ toolkit
The NCBI C++ Toolkit is a collection of C++ modules developed by the NCBI for writing bioinformatics software and applications.
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NCBI Education
What is bioinformatics? Why use bioinformatics? excellent tutorials on BLAST and the Entrez search and retrieval system.
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NCBI Human DNA Reference Sequence
Downloadable human DNA reference sequence as well as other reference genome sequences.
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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 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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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.
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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.
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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.
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NEBcutter
NEBcutter finds non-overlapping open reading frames and sites for all enzymes that cut the sequence just once; max length is 100 kb.
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NEMBASE2
NEMBASE2 is a database resource for EST datasets for 37 species of nematode. Sequences are clustered to redunce redundacy. Comparisons can be by library and at a sequence level; a visualisation tool is included. Coding region...
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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.
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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.
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NetPhhosK
The NetPhosK web-server produces neural network predictions of kinase specific eukaryotic protein phosphoylation sites.
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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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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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NEWT
NEWT is the taxonomy database maintained by the UniProt group.
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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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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.
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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...
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NNcon
Using 2D-recursive neural networks, NNcon is a web server for predicting protein contact maps.
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NOBAI
NOBAI web server facilitates the search for the evolutionary history embedded in the structure of functional RNA molecules.
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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...
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Non-Coding RNA database
Non-translatable RNA transcripts that appear to work at the RNA level.
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NORSp
NORSp (predictor of NOn-Regular Secondary Structure) is a tool for predicting disordered regions in proteins.
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NQ-Flipper
NQ-Flipper recognizes unfavorable rotamers of Asn and Gln residues in protein structures.
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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.
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NRSAS
Nuclear Receptor Structure Analysis Server (NRSAS) is a multi-purpose collection of tools for the analyses of nuclear hormone receptors.
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nsSNPAnalyzer
nsSNPAnalyzer is a tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) is phenotypically neutral or disease associated.
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NTMG
NTMG (N-Terminal Truncated Mutants Generator) is a tool for generating multiplex PCR primers for designing N-terminal truncated mutants.
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Nucleic Acids Research Database Issue
Molecular Biology Database Collection with links to databases with short descriptions of each.
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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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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.
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OGtree
Overlapping genes (OG) in prokaryotic species are used in OGtree to construct genome phylogeny trees. Overlapping gene content and overlapping gene order of the whole genome is used for the distance based method of tree const...
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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...
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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 ...
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Oligodb
Oligodb generates oligos suitable for expression experiments based on predicted gene transcripts from the Ensembl project. One can search for transcripts via keyword, or do a batch search by providing a list of Ensembl identi...
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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...
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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.
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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.
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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.
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Onto-CC
Gene Ontology Conceptual Clustering (Onto-CC) is a tool for independent validation of gene co-expression based on GO clusters.
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Ontology Lookup Service
The Ontology Lookup Service provides interactive and programmatic interfaces to query and browsea suite of biomedical ontologies and controlled vocabularies. Users can also navigate the relationships between terms and obtain ...
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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-...
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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.
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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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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...
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oPOSSUM
oPOSSUM is a web-based system for the detection of over-represented transcription factor binding sites in the promoters of sets of genes.
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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.
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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.
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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.
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OrfPredictor
OrfPredictor is designed for prediction of Open Reading Frames (ORFs) and coding regions of a batch of EST or cDNA sequences.
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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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Orthologue Search Service
BLAST a protein sequence then perform automated phylogenetic analysis to detect orthologous sequences.
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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.
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OSCAR
OSCAR (Open System for Clustering Analysis) is a platform for cluster analysis of microarray data.
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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.
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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 ...
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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.
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PaLS
Pathway and Literature Strainer (PaLS) highlights those members on a user inputted list that share descriptors from PubMed, GO, KEGG and Reactome.
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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...
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PAP
Promoter Analysis Pipeline (PAP) can identify potential transcriptional regulators for sets of co-expressed genes and identify potential regulatory targets of transcription factors.
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PAR-3D
PAR-3D (Protein Active site Residues - 3D structural motif) uses a structure-based approach for predicting function. Using 3D structural motifs defined for different classes of proteases, glycolytic pathway enzymes and metal-...
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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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Parasite-Genome
Parasite genome databases and genome research resources.
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PARSESNP
Project Aligned Related Sequences and Evaluate SNPs (PARSESNP) is a tool for the analysis of polymorphisms in genes.
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PartiGeneDB
PartiGeneDB is a database of about 300 partial genomes from eukaryotic organisms that have been assembled from EST data.
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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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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.
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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.
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Path-A
Pathway Analyst (Path-A) predicts and annotates pathways present in the query organism and provides a browsable database of ten currently supported metabolic pathways. Path-A can also take as input a list of protein sequences...
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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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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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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 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.
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PatSearch
PatSearch is a pattern matcher that is able to search for specific combinations of oligonucleotide consensus sequences, secondary structure elements and position-weight matrices.
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PatternHunter
PatternHunter is a general purpose sequence similarity search tool for DNA and protein sequences.
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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.
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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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PCE
PCE (Protein Continuum Electrostatics) is an interface to electrostatic potentials and pKa calculations using the MEAD package.
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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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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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PDB
Protein Data Bank; includes theoretical structures.
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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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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.
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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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PDBSiteScan
PDBSiteScan takes a PDB file as input, and searches for stuctural matches with the PDBSite set of known functional sites.
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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.
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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-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.
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PeptideMass
Cleaves a protein sequence with a chosen enzyme and computes masses of the generated peptides.
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PeptIdent
PeptIdent is a tool that allows the identification of proteins using pI, Mw and peptide mass fingerprinting data.
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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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Pfam
Collection of multiple sequence alignments and hidden Markov models covering many common protein domains.
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pFlexAna
Protein Flexibility Analyzer (pFlexAna) detects and displays conformational changes in remotely related proteins, without using sequence homology information. Rather than detecting regions of structural similarity, pFlexAna d...
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Pfold
The Pfold server takes an alignment of RNA sequences as input and predicts a common secondary structure.
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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.
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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...
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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...
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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.
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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.
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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...
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Phobius
Phobius is a combined transmembrane topology and signal peptide predictor. The server also allows for constrained and homology-enriched predictions.
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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.
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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...
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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 ...
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Phred/Phrap/Consed System
UNIX-based, base-calling, sequence assembly and finishing tools used by most genome sequence centres; free for non-commercial use.
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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...
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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.
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PHYLIP
Comprehensive set of programs for phylogenetic analyses; available for PC and Mac; source code available for easy compiling in UNIX.
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PhyloBLAST
BLAST a protein sequence, then perform automated phylogenetic analysis on hits or on uploaded sequences; PHYLIP-based analyses.
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PhyloDome
PhyloDome is a tool with which you can visualize and analyze the phylogenetic distribution of one or more eukaryotic domains.
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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...
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PhyloPars
The PhyloPars web server allows for easy, efficient estimation of metabolic parameters as inferred from observations on species that are phylogenetically related.
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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...
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PHYML
Phyml is a program that constructs phylogenetic trees from sequence alignments using the maximum likelihood method.
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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...
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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...
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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...
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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.
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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...
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PipMaker
PipMaker computes alignments of similar regions in two DNA sequences. MultiPipMaker allows the user to see relationships among more than two sequences.
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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.
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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.
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pKD
pKa Design (pKD) takes as input a protein structure and allows you to redesign the protein pKa value for that molecule. The server calculates a set of point mutations that will cause the desired pKa change.
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pKNOT
pKNOT (Protein Knot) is a tool that can detect knots in proteins as well as providing information on knotted proteins in PDB.
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PKNOTS
Predict pseudoknot structures in RNA sequence; source code only.
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pknotsRG
pknotsRG is a server for single sequence RNA secondary structure prediction including pseudoknots; source code, binary executable, and web service available.
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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.
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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...
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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; ...
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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...
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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...
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P-Match
P-Match is a transcription factor binding site identification tool that increases its accuracy by combining weight matrix and pattern matching approaches. Registration at the site is free and is required to use P-Match.
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PMG
The Protein Movie Generator (PMG) is a tool to generate protein pictures, animations, and movies.
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POBO
A server for the detection, comparison and verification of transcription factor binding site motifs in promoters. POBO bootstrap analysis applied to one or two clusters of co-regulated genes detects motifs under extreme level...
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POCO
POCO searches a set of promoters from co-expressed genes for nucleotide patterns that are over-represented.
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PolyBayes
UNIX-based SNP discovery from redundant sequences; integrated with Phred/Phrap/Consed infrastructure (see DNA -- Contig Assembly); free for non-commercial use.
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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.
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PolyPhred
UNIX-based tool for sequence trace based genotyping; integrated with Phred/Phrap/Consed (see DNA -- Contig Assembly); free for non-commercial use.
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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...
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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...
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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.
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POPS
Parameter OPtimised Surfaces (POPS) is an algorithm to calculate accessible surfaces areas at atomic and residue level.
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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.
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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 ...
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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...
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POV-Ray
Persistence of Vision Raytracer; use in conjunction with Swiss-PdbViewer to create graphics for presentation and publication.
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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...
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POXO
POXO is a series of tools that can be used to discover, search, and verify transcription factor binding sites (TFBS) from sets of co-expressed genes.
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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...
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PPG
The Protein Picture Generator (PPG) is a tool for making pictures (and animations) of protein structures from PDB files.
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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...
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Practical Structural Databases
Detailed compendium of links to structure databases, viewers, tools.
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PRALINE
Praline is a multiple sequence alignment program that can integrate information from sequence similarity searches and secondary structure prediction.
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PrDOS
PrDOS (Protein Disorder Prediction Server) is a server to predict the disordered regions of a protein from its amino acid sequence.
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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.
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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.
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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...
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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 ...
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Predikin
The Predikin web server allows users to predict substrates of protein kinases. Users input a protein kinase for evaluation
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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...
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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...
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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...
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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...
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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.
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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 ...
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Primer3
Comprehensive PCR primer and hybridization probe design tool; many options but easy to accept defaults at first.
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Primer3Plus
Primer3Plus is an enhanced web interface to the popular Primer3 PCR primer design program.
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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...
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PrimerStation
PrimerStation is a multiplex genomic PCR primer design tool specific for the human genome.
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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.
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PRISM
PRISM (PRotein Interactions by Structural Matching) is a tool for analysing protein interfaces and predicting protein-protein interactions.
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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...
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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 ...
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PRODOC
PRODOC is a repository of domain assignments from Pfam for proteins encoded in different complete genomes and a tool for querying this information.
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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...
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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.
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PROFEAT
Protein Features (PROFEAT) is a tool for computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence.
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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.
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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.
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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...
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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...
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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...
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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...
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PromAn
PromAn is an integrated promoter analysis platform that takes a genomic sequence of interest and considers information on orthologous genomic sequence(s), user submitted patterns, and public databases to predict transcription...
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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.
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PromH
PromH predicts transcription start sites (TSS), TATA boxes, and transcription factor binding sites (TFBS) in promoter regions using pairs of orthologous sequences.
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ProMiR II
Probabilistic miRNA prediction (ProMiR) is a resource that includes: ProMiR-v to search for both conserved and non-conserved miRNAs in the vicinity of a known miRNA; ProMiR-c to predict both conserved and non-conserved miRNAs...
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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.
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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...
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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...
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PromoterWise
Compares two DNA sequences allowing for inversions and translocations, ideal for promoters.
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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
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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.
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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.
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PROSITE
Database of protein families and domains defined from SwissProt database; consider also checking specific motif databases such as PhosphoBase.
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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...
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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.
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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...
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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.
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ProTarget
ProTarget offers a method for the prediction of novel structural superfamilies by assessing the relationship of input protein sequences to previously solved 3D structures.
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ProteDNA
ProteDNA identifies the sequence-specific binding residues in a transcription factor, protein-DNA interaction.
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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...
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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...
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Protein Dipole Server
The Protein Dipole server calculates and displays the net charge, dipole moment and mean radius of any 3-dimensional protein structure.
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Protein Peeling
Protein Peeling is an approach for splitting a protein three dimensional (3D) structure into protein units, an intermediate level of protein structure description between protein domains and secondary structures.
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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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ProteMiner-SSM
ProteMiner-SSM searches the PDB for proteins with similar tertiary substructures to one specified by the user. A filtering process is used to significantly speed up the analysis.
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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 Analysis at EBI
The Proteome Analysis Database at EBI provides statistical and comparative analyses of the predicted proteomes of organisms for which there are fully-sequenced genomes.
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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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ProteomicsSURF
ProteomicsSURF is a site dedicated to disease proteomics which aims to identify proteins involved in human disease and to understand how their expression, structure and function cause illness.
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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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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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(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 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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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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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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PubChem
PubChem contains the chemical structures of small organic molecules and information on their biological activities. PubChem can be searched by keywords, chemical properties, and structural similarity. PubChem's chemical ...
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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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PubFinder
PubFinder is a tool to facilitate searching through PubMed abstracts. The user chooses a set of abstracts that are representative of the subject area of their search. PubFinder then uses words from the selected abstracts to s...
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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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PUNS: Primer-UniGene Selectivity Testing
The Primer-UniGene Selectivity Testing software system (PUNS) assists in the specificity design of PCR primers. A set of primers must be physically designed first. Then PUNS can be used to estimate the expected number of diff...
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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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PupasView
PupasView takes a single gene identifier as input and reports SNPs that have the potential to affect phenotype. In addition to looking for potential amino acid changes, PupaSNP also searches for SNPs with the potential to aff...
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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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pvSOAR
pvSOAR takes a PDB ID or structure file as input, and searches for other proteins with surface regions that are similar to the query structure.
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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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QPPD
QPPD (Quantitative PCR Primer Database) contains information about primer sets published for quantitative PCR assays. This database can be searched by gene name, keyword, or by identifier. Results return primer sequences, gra...
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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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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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Rat BAC Ends
TIGR BAC end sequencing project; query genomic sequence or clone name against database of BAC end sequences to find set of minimally overlapping clones; BACs are same as those fingerprinted by Genome Sciences Centre, Vancouve...
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Rat BAC Physical Map
BAC fingerprint map of the rat genome, by Genome Sciences Centre, Vancouver.
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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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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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Reactome - a knowledgebase of biological processes
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
The Restriction Enzyme Database, a collection of information about restriction enzymes and related proteins.
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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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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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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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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; oth...
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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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RE-MuSiC
RE-MuSiC is a tool for multiple sequence alignments where users can specify conserved blocks by supplying regular expression contraints.
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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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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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Resourcerer
Tool for cross-referencing microarray data derived from different species and across different expression analysis platforms. Built using the analysis of ESTs, the TIGR Gene Index (TGI), and Eukaryotic Gene Orthologs (EGO) da...
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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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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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RiceTFDB
RiceTFDB(Rice Transcription Factor DataBase) is a database of sequences and alignments for transcription factors in Rice.
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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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RNAbase
RNAbase is a searchable and annotated database of all publicly available RNA structures.
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RNABindR
RNABindR is a server for analyzing and predicting RNA binding sites in proteins.
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RNABOB
Fast RNA motif/pattern searcher; from the authors: If you re looking for an RNA motif that fits a hard consensus pattern -- a la PROSITE patterns, but with base-pairing -- you might check out RNABOB; not a Web-tool; based on ...
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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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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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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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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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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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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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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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RSRE
RNA Structural Robustness Evaluator (RSRE) is a tool for RNA structural robustness evaluation.
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RTAnalyzer
RTAnalyzer is an application to find new retroposons and detect L1 retroposition signatures.
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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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SAGExplore
SAGExplore is a tool for the accurate mapping of experimental tags in serial analysis of gene expression (SAGE).
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SAKURA
SAKURA is the DDBJ DNA Database Submission System.
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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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SAM-T08
The SAM-T08 web server is a 3D protein structure prediction server. The server also provides 3 multiple sequence alignments of putative homologs, prediction of local structural features including backbone and burial propertie...
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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.
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SARSA
SARSA is a web tool for the alignment of two or more RNA tertiary structures. Users input 3D RNA structures in PDB format and SARSA returns a graphical display of the alignment.
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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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Satellog
Satellog is a database for the identification and prioritization of satellite repeats in disease association studies.
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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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Science.bio.org News
Archived daily news source for current events in biotechnology.
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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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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.
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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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SDPMOD
SDPMOD is a comparative modelling tool for small disulfide-bonded proteins (SDPs).
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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...
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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.
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SEARCHPKS
SEARCHPKS is a program for the detection and analysis of Polyketide Synthase (PKS) domains.
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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...
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seeMotif
The web server seeMotif allows users to interactively visualize sequence motifs on protein structures from Protein Data Bank (PDB).
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Selecton
Selecton is a server for the identification of site-specific positive selection and purifying selection.
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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...
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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.
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SEPACS
SEPACS (Seroreactivity Pattern Classification System) is a a web-based application for classification of seroreactivity profiles.
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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.
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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...
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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...
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Sequence Harmony
Sequence Harmony detects subfamily specific functional sites from a multiple sequence alignment by scoring compositional differences between given subfamily groupings.
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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.
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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...
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The Sequence Ontology Project
The Sequence Ontology Project aims to provide a standard vocabulary for describing biological sequences.
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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).
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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...
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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...
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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; ...
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Services from Zhou Laboratory
Tools from the Zhou laboratory including predictors of transmembrane topology (THUMBUP, UMDHMM-TMHP, TUPS); prediction/analysis tools for tertiary structure (SPARKS2, SP3); and, prediction/analysis tools for interactions (DMO...
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SeWeR
Sequence analysis tools on the web; includes nucleic acid, protein, PCR and alignment tools.
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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...
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SGD
The Saccharomyces Genome Database.
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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...
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SH3-Hunter
SH3-Hunter identifies putative SH3 domain interaction sites on protein sequences.
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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.
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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.
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SIFT
Sorting Intolerant From Tolerant (SIFT) is a sequence homology-based tool that will predict whether an amino acid substitution will affect protein function.
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SignalP
Prediction of presence and location of signal peptide cleavage sites in amino acid sequences.
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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...
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SIM4
Align cDNA with genomic DNA, allowing for introns and small number of sequencing errors.
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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).
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siRNA Selection Server
Server aiding the design of short interfering RNAs (siRNAs) by providing information on stability, SNPs and specificity of the a potential siRNA.
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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.
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SITECON
Server for the detection of conformational and physicochemical properties in transcription factor binding sites and potential binding sites.
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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...
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SiteFINDER|3D
SiteFINDER|3D predicts functionally important regions in proteins of known structure using conserved functional group (CFG) analysis.
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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 (...
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SiteSeer
SiteSeer is a visualization tool for mapping transcription factor binding sites (TFBS) in the upstream regions of single or grouped eukaryotic genes.
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siVirus
siVirus aids in the design of short interfering RNA (siRNA) and helps to identify conserved target sequences for antiviral RNA interference.
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SLAM
SLAM is a comparative-based annotation and alignment tool for syntenic genomic sequences that performs gene finding and alignment simultaneously. SLAM also predicts CNSs (conserved non-coding sequences).
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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.
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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.
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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.
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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...
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snoGPS
snoGPS allows you to search for H/ACA snoRNA (small nucleolar RNA) genes in a genomic sequence
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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...
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snowdeal.org > {bio,medical}informatics
A weblog that provides daily updates and links to news items and stories of interest to bioinformatics community.
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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...
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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.
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SNP Cutter
SNP Cutter is a tool that automates PCR-RFLP assay design for SNP genotyping.
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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...
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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.
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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...
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soaPDB
soaPDB is a web application for the generation and organization of saved PDB searches as well email notifications.
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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 ...
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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...
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SOP3v2
SOP3v2 takes a list of gene names, a list of reference sequence IDs or a chromosomal location as input and provides a set of PCR and sequencing primers as output. These primers are optimized for sequence-based genotyping assa...
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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.
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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.
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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.
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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.
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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...
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S. pombe genome
Schizosaccharomyces pombe Genome Sequencing Project.
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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...
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Spritz
Spritz is a tool for the prediction of disordered regions of proteins.
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Sride
Sride is a tool for identificating stabilizing residues in protein structure.
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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.
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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).
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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.
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SSR Primer
Simple Sequence Repeats (SSR) Primer aids in design of primers that can amplify microsatellite sequences. SPUTNIK is used to screen for SSR and Primer3 for locus specific primer design. Precomputed results can be viewed using...
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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...
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SStructView
RNA secondary structure viewer applet; must be integrated into web page to be implemented; can link to multiple computational backends.
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Staden Package
UNIX-based tools for sequence assembly, mutation detection and sequence analysis; free for non-commercial use. Note that Staden development and support have ceased due to lack of funding, despite widespread use.
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STAMP
STAMP is a tool for exploring DNA-binding motif similarities by providing resources for motif alignment, similarity and database matching.
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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.
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Statistics.com
Online statistics courses. Also contains links to statistics software and on-line textbooks.
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Statistics Notes in the British Medical Journal
Brief descriptions of statistical concepts and methods often combined with clinical/medical examples.
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STING Millenium
STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them.
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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...
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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...
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STREAM
Static Thermodynamic REgulAtory Model of transcription - a bioinformatics application for researchers, who want to model the transcriptional regulation of a specific gene and predict its transcriptional output in different si...
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STRIDE
STRIDE takes a PDB structure as input and reports back either secondary structure assignments, a Ramachandran plot or a contact map.
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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...
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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.
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Stubb
Stubb uses a probabilistic model and a maximum likelihood approach to detect clusters of transcription factor binding sites (TFBS) in genomic sequences (limit of 100 Kb). It can also use related genomes to improve module pred...
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SUMOsp
SUMOylation Sites Prediction (SUMOsp) predicts sites for sumoylation, a reversible post-translational modification of proteins by the small ubiquitin-related modifiers (SUMO).
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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...
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SuperLooper
SuperLooper is a web tool for the modeling of loops in globular and membrane proteins.
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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...
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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. Such information can be useful in drug classification and target ...
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SVC
SVC (Structured Visualization of Evolutionary Conserved Sequences) is a tool that can search for pairs of orthologous genes, align the protein coding sequences, and visualize the evolutionary sequence conservation mapped back...
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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...
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SVM-PROT
Support Vector Machine of Proteins (SVM-PROT) is a tool for predicting and classifying protein families.
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SVMtm
Support Vector Machine Transmembrane (SVMtm) predicts transmembrane helices when given protein sequences in FASTA format.
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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.
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SWISS-2DPAGE
This is a 2D gel electrophoresis database containing data for proteins identified on SDS-PAGE or 2D-PAGE reference maps.
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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.
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Swiss Model
Automated protein modelling server.
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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).
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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.
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Swiss-Shop
Submit sequence, pattern or keywords to receive email alert when new sequences of interest appear in SwissProt.
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SymAtlas
SymAtlas is a web-application for displaying reference microarray data sets on commercial Affymetrix platforms.
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SymmDock
SymmDock is an server for prediction of complexes with cyclically symmetry by geometry based molecular docking.
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SynoR
SynoR searches vertebrate genomes for synonymous regulatory elements.
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Nucleic Acids Research

NAR Web Server Summaries - Alphabetical List