Compilation Paper Category List Alphabetical List Category/Summary List Search Summaries Bioinformatics Links Directory NAR Web Server Summaries - Alphabetical List
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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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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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-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-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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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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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-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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Protein fold recognition using 1d and 3d sequence profiles coupled with secondary structure and solvation potential information.
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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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3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.
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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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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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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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3Motif is a tool for visualizing protein sequence motifs and their properties in 3 dimensions from PDB structure files.
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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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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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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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The Quick Guide includes descriptions of more than 150 organisms and has links to sequencing centers and scientific abstracts.
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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Annotation of MIcrobial Genes (AMIGene) is gene prediction server that can identify coding sequences in microbes.
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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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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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Amos WWW links page
Extensive list of links to biology resources; compiled by Amos Bairoch of SWISS-PROT.
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Extensive list of links to biology resources; compiled by Amos Bairoch of SWISS-PROT.
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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 (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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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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The AS2TS (Amino acid Sequence to Tertiary Structure) system consists of servers for protein structure analysis and modelling.
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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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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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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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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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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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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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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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Assembly PCR Oligo Maker is a tool for designing oligodeoxynucleotides for the PCR based construction of long DNA molecules.
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Association for Studies in Computational Biology
The Association for Studies in Computational Biology (ASICB) website is a Bioinformatics portal with a focus on news and initiatives in India. The Knowledge Base section of the website has great summaries of key topics in bio...
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The Association for Studies in Computational Biology (ASICB) website is a Bioinformatics portal with a focus on news and initiatives in India. The Knowledge Base section of the website has great summaries of key topics in bio...
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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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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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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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AthaMap is a genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana
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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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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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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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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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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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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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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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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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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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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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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 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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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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BhairPred is a tool for predicting beta-hairpins in protein sequences using a support vector machine.
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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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Stores full descriptions of interactions, molecular complexes and pathways; researchers are able to submit new records.
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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 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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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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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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Bio-IT World
BIO IT technology trends & forecasts, industry news & analysis, bioinformatics and drug discovery updates.
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BIO IT technology trends & forecasts, industry news & analysis, bioinformatics and drug discovery updates.
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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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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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BioBayesNet is a server for feature extraction and Bayesian network modeling of biological sequence data.
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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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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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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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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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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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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 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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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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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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BioJava
The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.
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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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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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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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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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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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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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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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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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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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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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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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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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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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BioPipe
The biopipe is a workflow framework that seeks to address some of the complexity involved in carrying out large scale bioinformatics analysis. It has been designed to work intimately with the bioperl package.
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The biopipe is a workflow framework that seeks to address some of the complexity involved in carrying out large scale bioinformatics analysis. It has been designed to work intimately with the bioperl package.
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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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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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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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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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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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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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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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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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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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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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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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BLAST2SRS
BLAST2SRS (Sequence Retrieval System) is a tool to retrieve protein sequences using similarity (BLAST) and keyword searches.
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BLAST2SRS (Sequence Retrieval System) is a tool to retrieve protein sequences using similarity (BLAST) and keyword searches.
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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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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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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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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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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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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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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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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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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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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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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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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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The MGuide (version 2.0). The Brown Labs complete guide to microarraying for the molecular biologist.
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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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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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caBIO Web Services
SOAP interfaces used to access the cancer Bioinformatics Infrastructure Objects(caBIO) funtionality.
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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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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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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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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 Course Listings
A list of bioinformatics courses available at Canadian post-secondary institutions.
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A list of bioinformatics courses available at Canadian post-secondary institutions.
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Canadian Bioinformatics Programs
A list of bioinformatics programs available at Canadian post-secondary institutions.
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A list of bioinformatics programs available at Canadian post-secondary institutions.
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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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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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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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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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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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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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CAPweb
CGH array Analysis Platform (CAPweb) is a tool for storing, analyzing and visualizing CGH-array data.
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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Contains numerous articles concerning the legal and ethical issues arising from the developments in genetic technology.
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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cisRED is a database system for genome-scale computational discovery of regulatory elements.
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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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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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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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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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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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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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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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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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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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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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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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COnsensus-DEgenerate Hybrid Oligonucleotide Primers (CODEHOP); degenerate PCR primer design; will accept unaligned sequences.
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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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Find GC content and frequency of codon usage for any organism that has a sequence in GenBank.
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CodonO
CodonO is a method for measuring synonymous codon usage bias within and across genomes.
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CodonO is a method for measuring synonymous codon usage bias within and across genomes.
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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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Clusters of Orthologous Groups represent ancient conserved protein domains; use COGnitor tool to find COGS in sequence of interest.
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Color Base Pair
On-line bioinformatics resources including links to news, forums, tutorials, and jobs.
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On-line bioinformatics resources including links to news, forums, tutorials, and jobs.
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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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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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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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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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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.
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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.
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Computational Biology Institute of Ontario
Home of the Ontario community of Computational Biologists
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Home of the Ontario community of Computational Biologists
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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.
website summary
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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 (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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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excellent online genetics activities, including BioServers bioinformatics tools designed for teachers and students, and animations explaining techniques such as PCR.
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DNA Methylation Database
The database contains information about the occurrence of methylated cytosines in the DNA.
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The database contains information about the occurrence of methylated cytosines in the DNA.
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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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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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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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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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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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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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Doelan is an tool designed to monitor the quality of DNA microarray production.
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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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DOMAC is an accurate, protein domain prediction server that integrates homology modeling, domain parsing, and ab initio methods together.
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Dotlet
Dot plot tool with very helpful learn by example interpretations of sample outputs.
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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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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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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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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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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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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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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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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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DSSPcont automates protein secondary structure prediction from PDB structures to reflect structural variations due to thermal fluctuations.
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DTFAM
Dragon TF Association Miner (DTFAM) is text-mining tool which takes Pubmed abstracts/summaries as input and reports potential associations between transcription factors and diseases/GO ontologies. The user can also provide a ...
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Dragon TF Association Miner (DTFAM) is text-mining tool which takes Pubmed abstracts/summaries as input and reports potential associations between transcription factors and diseases/GO ontologies. The user can also provide a ...
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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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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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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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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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E. coli Genome Project
U.Washington E. coli genome project site maintains and updates the annotated sequence of the E. coli K12 genome; also has resources and tools for functional characterization of E. coli genes
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U.Washington E. coli genome project site maintains and updates the annotated sequence of the E. coli K12 genome; also has resources and tools for functional characterization of E. coli genes
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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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 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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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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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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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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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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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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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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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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The Rat Genome project is an international collaboration to sequence the genome of the brown rat (Rattus norvegicus).
website summary
Ensembl Zebrafish Genome Browser
This ensembl website features the zebrafish whole genome shotgun assembly sequence.
website summary
This ensembl website features the zebrafish whole genome shotgun assembly sequence.
website summary
EnteriX
EnteriX is a collection of tools for viewing pairwise and multiple alignments for bacterial genome sequences.
website summary
EnteriX is a collection of tools for viewing pairwise and multiple alignments for bacterial genome sequences.
website summary