Bioinformatics & Genomics
Companies, Publishers, & Books
Compendiums & Lists of Resource Links
Compounds & Enzymes
Educational & Information Resources
Genomics & DNA Sequence Analysis
Hidden Markov Models
Major Sites & Organizations
Metabolic Pathway Databases & Related
Molecular Modeling & Visualization
Motif, Domain, Profile, Pattern, & Repeat Searches
Multiple Alignment & Phylogeny
Protein & Nucleic Acid Search Servers
Protein Analysis from Sequence
Sites with Multiple or Integrated Tools
Software Catalogues, Lists, & Downloads
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A. C. R. Martin Bioinfo Site
Downloadable Java software for bioinformatics, including a Needleman-Wunsch program and a protein structural least-squares fit program.
[Univ. of Michigan] (Naohiro Inohara) Analyzes DNA and protein sequences.
Analytical Biostatistics Section
[NIH] The ABS offers downloadable software and servers in the areas of sequence analysis, protein structure prediction, ligand binding, and gene expression.
BCM Gene Finder
[Baylor College of Medicine] This service provides several tools that use the identification of certain regions (splice sites, protein coding exons, promotor and poly-A regions) in nucleic acid sequences to find possible genes.
BCM Search Launcher
[Human Genome Center, Baylor College of Medicine] A collection of molecular biology-related search and analysis services available on the WWW. Currently connects to a general protein sequence, or protein pattern searches, species-specific protein sequence searches, nucleic acid sequence searches, multiple sequence alignments, pairwise sequence alignments, gene feature searches, sequence utilities, and protein secondary structure prediction.
Bioinformatics & Pattern Discovery
[IBM] Information and bioinformatics related servers developed at IBM. Services include sequence pattern analysis, gene expression analysis, and multiple sequence alignment. Servers may be used online, or the code may be downloaded.
Bioinformatics and Biological Computing
[Weizmann Institute of Science] This is home for a wealth of tools, databases, and information in bioinformatics. There are servers in the areas of sequence analysis, proteomics, and genomics, as well as downloads and educational products. The Crown Human Genome Center is also part of this site.
BioInformatics and Molecular Analysis Section
[NIH] BIMAS offers many bioinformatics tools, including DNA sequence analysis, a mirror of GeneCards, genetic linkage analysis, and more. A catalog of linkage analysis software is also provided.
[National University of Singapore] A comprehensive site providing information and multiple bioinformatic related analysis tools in areas such as phylogenetics, lab management, and metabolic pathway visualization.
Bioinformatics(Computational Biology) Group
[University of California Santa Cruz] This group is dedicated to the discovery and implementation of algorithms that facilitate the understanding of biological processes. Members study the primary (sequence), secondary (folding), and tertiary (3-dimensional) structures of DNA, RNA, and protein sequences. A number of servers and databases in these areas are provided, as well as educational materials.
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[UCSD San Diego Supercomputer Center] The WorkBench allows biologists to search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems.
Biomolecular Structure and Modelling Group
[University College London] The BSM group brings together people who derive protein and carbohydrate structure information using crystallography or NMR, those who manage databases of this information, and analysts and modellers who examine these structures to try to derive principles of protein folding. Services are offered in the areas of protein sequence and stucture analysis. The group is the home of the CATH protein structure classification database.
Computer based biological research via the internet. Bionatigator is a virtual bioinformatics workspace that puts a comprehensive range of internet-delivered research tools into the
hands of biologists. You control your data, your analyses and your
output, in real time and reproducibly. Running programs on BioNavigator is fee based.
The Brutlag Bioinformatics Group
[Stanford University] This group is interested in the
problems of predicting biological function of genes and proteins from their primary sequence (sometimes known as functional genomics), predicting structure of protein and DNA from its sequence, and understanding how and when genes are expressed. This site links to tools being developed toward these interests.
[Celera] Celera Corporations scientific home page that provides Celera and related biotechnology news and password access to the Celera Discovery System of genomic databases and analysis tools.
Center for Biological Sequence Analysis
[Technical University of Denmark] CBS conducts basic research in bioinformatics. It offers a number of nucleotide and protein prediction (from sequence) servers, other tools, and "value-added" datasets.
Center for Molecular Modeling
[NIH] CMM is a major supplier of molecular modeling resources and
expertise to the NIH research community. The site contains many annotated links to bioinformatics resources and tutorials.
Centre for Molecular and Biomolecular Informatics
[Univ. of Nijmegen] Information on multiple bioinformatics related services, research, and program courses at this center.
Comparative RNA Web Site
[University of Texas] A comprehensive site with information on RNA including methods in structure prediction, RNA sequence/structure database, RNA structure information, RNA structure analysis, and rRNA structure-based phylogeny.
[Oak Ridge National Laboratory] We conduct genetics research and system development in genomic sequencing, computational genome analysis, computational protein structure analysis, high-performance biocomputing, bioinformation systems, biosystems modeling, and genetics information management.
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Computational Biology and Informatics Laboratory
[University of Pennsylvania] Multiple bioinformatics related tools and databases. The site also includes information about related degree programs and UPenn.
Computational Biology Tools
[Cornell Theory Center] This site provides several downloadable programs for analyzing protein sequences for predictions in the areas of folding, structure determination, energetics, and dynamics. It also is home to the LOOPP program (Learning, Observing and Outputting Protein Patterns), a program for potential optimization and alignments. LOOPP aligns sequence to sequence, sequence to structure, and structure to structure.
Computational Services at EMBL
[EMBL] Ties together sequence search and retrieval, alignment, data submission, comparison and prediction into one site. Also available are tools for structure verification and related software.
CUBIC: Columbia University Bioinformatics Center
CUBIC contains a wealth of services, databases, articles and their data sets, and annotated bioinformatics links. It is the current home of PredictProtein and other services for protein analysis.
DARWIN Molecular Sequence Analysis
[CBRG] An interactive tool for peptide and nucleotide sequence analysis with a library of functions for sequence management and analysis, statistics, numerics, and graphics.
DDL - Drug Design Laboratory
[Milan University, Italy] This site presents downloadable programs for drug design, including molecular dynamics for solvated molecules, program Predator to predict secondary structure of proteins, and molecular orbital calculations.
[Carlsberg Laboratory] Software for handling and analysis of nucleotide and protein sequences.
This downloadable package also has special functions for EST and SAGE handling and analysis.
[European Molecular Biology Network - Swiss Node] This site provides DNA and protein sequence analysis tools, sequence alignment tools, and other bioinformatics tools. It also provides numerous links to related information, courses, universities, and documentation.
[Swiss Institute of Bioinformatics] The EXPASy "server is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE." This site contains links to databases, tools and software packages, education and services, documentation, lists of links to molecular biology resources, links to major molecular biology servers, and local links.
[Nature Technology Corporation] A comprehensive site with links to information and resources in biotechnology and bioinformatics. The large number of resource categories include academic sites, conferences, employment, genomics, proteins, grants & contracts, intellectual property, methods & protocols, software, and venture capital.
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GeneCensus Genome Comparisons
[Yale University] This site provides genome and phylogenetics related information, databases, and services for many classes of organisms, mainly microscopic.
[European Bioinformatics Institute] "GeneQuiz is an integrated system for large-scale biological sequence analysis, that goes from a protein sequence to a biochemical function, using a variety of search and analysis methods and up-to-date protein and DNA databases."
[CuraGen] This commercial sites offers a fully integrated genomics suite of
services, including discovery-oriented software for SeqCalling with sequence and SNP data, GeneCalling with gene expression data, PathCalling with protein -protein interactions and pathways, a pharmacogenomics database of drug profiles, and SNPCalling with our database of 200,000 cSNPs (gene-based single nucleotide polymorphisms).
[IGH Montpellier France] A list of tools including sequence comparison, sequence anotation, and peptide fingerprinting.
GenomeNet WWW server
[Institute for Chemical Research, Kyoto University] A Japanese network of database and computational services for genome research and related research areas in molecular and cellular biology.
[Oak Ridge National Laboratory] A suite of tools designed to provide analysis and putative annotation of DNA sequences interactively and using automated computation. GRAIL supports e-mail and interactive graphical sessions.
Institute of Biology and Chemistry of Proteins
The aim of the research at the IBCP is to study proteins in their biological context. These studies are concerned with both intracellular and extracellular proteins of procaryotic and eucaryotic organisms dealing mainly with biosynthesis, maturation, and interactions. The IBCP is the home of Network Protein Sequence Analysis and software for protein sequence analysis.
[European Bioinformatics Institute] InterPro is an integrated documentation resource for protein families, domains and
sites, developed initially as a means of rationalising the complementary efforts of the
PROSITE, PRINTS, Pfam and ProDom database projects. Each combined InterPro
entry includes functional descriptions and literature references, and links are made
back to the relevant member database(s), allowing users to see at a glance whether
a particular family or domain has associated patterns, profiles, fingerprints, etc.
ISREC Bioinformatics Group
[Swiss Institute for Experimental Cancer Research] "Our main field of research is the detection and assessment of similarity between distantly related protein and DNA sequences by means of 'Generalized Profiles.' We have developed and made available a program package that allows searches with a single sequence against a database of generalized profiles and vice versa."
ISREC Software Homepage
[Swiss Institute for Experimental Cancer] This site provides a number of servers in the areas of sequence analysis, domain/motif searches, gene prediction, and prediction of protein features.
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[Incyte Gemomics] LifeSeq provides fee access to Incyte's human gene sequence databases, complete with integrated bioinformatics tools.
[Columbia University Bioinformatics Center] This server submits your protein sequence to other servers through one interface. Analyses are in the areas of protein structure and function.
Network Protein Sequence @nalysis
[Institute of Biology and Chemistry of Proteins] [email protected] is an interactive Web server dedicated to protein sequence analysis. Analyses offered include sequence similarity, site detection, multiple alignment, secondary structure prediction, and primary structure analysis. Analyses can be combined in a pipeline. The ANTHEPROT windows program is also available here.
Nucleotide Sequence Analysis
[Sanger Centre] This server provides multiple nucleotide sequence analysis tools that will identify splice sites, protein coding exons, promotors, poly-A regions, and more.
PANAL Protein Analysis
[University of Minnesota] PANAL is an integrated resource for protein sequence analysis. The tool allows the user to simultaneously search a protein sequence for motifs from several databases, and to view the results as an intutive graphical summary.
[consortium of several research laboratories] This genomics site is oriented to plant functional genomics. The site maintains servers for analyzing protein sequence, searching for patterns, and plotting motifs. The site also discusses plant protein phosphorylation.
[EMBL] Permits the user to submit a sequence for prediction. Links to other pages for multiple sequence alignment, prediction of secondary structure, prediction of solvent accessibility, prediction of transmembrane helices, prediction of topology for transmembrane proteins, fold recognition by prediction-based threading, and evaluation of secondary structure prediction accuracy.
Protein Secondary Structure Prediction Tools
[ExPASy] An annotated list of links to a number of tools that provide protein secondary structure prediction.
Protein Sequence Analysis Launcher
[Swedish Foundation for Strategic Research] At ProSAL you paste a single protein sequence and are offered analyses in the following areas: sequence similarity (local and global), domain and motif searches, and predictions of chemical and structural properties.
Protein Tertiary Structure Tools
[ExPASy] An annotated list of links to tools that provide 3D protein folding and modelling.
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Proteomics & Bioinformatics
[Samuel Lunenfeld Research Institute] "Canada's Premiere Research Center for Proteomics and Bioinformatics" provides several tools and downloadable programs for protein sequence analysis.
[ExPASy] An extensive annotated list of links to tools that provide analysis of protein sequences and structures.
[Munich Information Center for Protein Sequences] ProtFam by MIPS is a curated protein classification database. In a joint effort, MIPS and
PIR-NBRF classify sequences into
superfamilies and families and annotate homology domains. This is part of the joint project to
produce the PIR-International Protein Sequence Database.
Regulatory Sequence Analysis Tools
[Laboratory of Computational Biology] A series of modular computer programs specifically designed for analyzing sequences of Saccharomyces cerevisiae .
The RNA World Website
[IMB-JENA] An extensive list of links to RNA related databases and web tools.
The rRNA WWW Server
[Univ. of Antwerp, Belgium] Links to the LSU rRNA Database (aligned sequences from the large subunit rRNA); the SSU rRNA Database (aligned sequences from the small subunit rRNA); DCSE (multiple sequence alignment editor) Home Page; TREECON (tree construction); and TRAFOR (format conversion).
The Sanger Centre
The Sanger Centre is a genome research centre founded to further the knowledge of genomes, particularly through large scale sequencing and analysis.
[ExPASy] Allows the user to browse through a number of databases, such as SWISS-PROT, PROSITE, SWISS-2DPAGE, SWISS-3DIMAGE, ENZYME, CD40Lbase, and SeqAnalRef; as well as other cross-referenced databases (EMBL/GenBank/DDBJ, OMIM, Medline, FlyBase, ProDom, SGD, and SubtiList). It also allows access to many analytical tools for the identification of proteins, the analysis of their sequences, and the prediction of their tertiary structures.
Search and Analysis
[DDBJ] A short list of links to common DNA and protein sequence analysis tools.
Sequence Alignment Utility
[MIPS] Performs pairwise alignments for PROTEIN or DNA sequences.
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Sequence Manipulation Site
The Sequence Manipulation Suite is a collection of web-based
programs for analyzing and formatting DNA and protein sequences. The output of each program is a set of HTML commands, which is
rendered by your web browser as a standard web page. You can print
and save the results, and you can edit them using an HTML editor or a
The Southwest Biotechnology and Informatics Center (SWBIC)
SWBIC provides a single-point access to a vast store of widely distributed biotechnology information as well as developing new educational and bioinformatics services. You are in SWBIC's Internet Resources Search.
SRS: Sequence Retrieval System
[European Bioinformatics Institute] A network browser for databanks in molecular biology. Searches sequence libraries too numerous to list here.
[The Barton Group] A suite of programs for the comparison and alignment of protein three dimensional structures. The suite will multiply align structures and produce a corresponding sequence alignment with confidence values associated with each aligned position.
Stanford Genome Technology Center
[Stanford University] This site provides information about the center's informatics projects and links to DNA sequencing projects, software, and tools.
UCLA-DOE Structure Prediction Server
[UCLA] Provides protein fold recognition, sequence analysis, and validation. Output data is formatted in HTML.
UK Human Genome Mapping Project Resource Center
[HGMP] "The UK Human Genome Mapping Project Resource Centre (HGMP-RC) provides access to leading-edge tools for research in the fields of genomics, genetics, and functional genomics."
Virtual Genome Center
An online resource for accessing tools and databases for Molecular Biologists.
[Argonne National Laboratories] "WIT is a www-based system to support the curation of function assignments made to genes and the development of metabolic models."
[University of Manitoba] A collection of tools designed enable the user to identify, extract, and manipulate data from major databases such as GenBank, EMBL and PIR.
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