World of Bioinformatics Links

I've tried to make this page have some sort of structure, rather than just list loads of links one after another. Also, we do (that's "we" in the lab here) use a lot of these links and thus they have been included here as we have found them useful. I've tried to not to include links just for the sake of including links. These links relate to the areas of what we do in our lab (if you are interested in a slighly more general (and therefore a lot longer) list of Bioinformatics links then I would suggest you try this list of links at the University of Texas Health Science Center at San Antonio.

All links have been tested at the time of writing. If you find a link that has expired, or would like to nominate a link to add to these then please let me know. Some links have been deliberately included more than once where they relate strongly to more than one subject heading.

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The following table lists major subject headings on the left, with their respective subcategories on the right. Select a link to go to a list of sites that relate to that heading.



Bioinformatics Databases
  • Protein
  • Nucleotide
  • Protein Structure
  • Other

    • Sequence Searching, and Sequence Retrieval
  • SRS sites
  • Other search sites
    		•

    General Bioinformatics Sites
  • Academic sites
  • Corporate/Government
    		•

    Subject Specific Sites
  • Codon Usage
  • Computing, Software, etc.
  • Correspondence Analysis
  • Genome Analysis, Genomic Comparisons
  • Phylogenetics
    		•

    Model Organisms
  • HIV
  • Escherichia coli
  • Haemophilus influenzae
  • Yeast
  • Caenorhabditis elegans
  • Mouse
  • Human
    		•

    Related Journals

    Bioinformatics Databases

    Protein

  • The OWL database - Non-redundant protein database
  • PIR databases - Protein Information Resource
  • SWISS-PROT
  • PDB - Protein Data Bank (at Brookhaven National Laboratory

    Nucleotide

  • GenBank database
  • GenBank Latest Release Information
  • BankIt - Info on submitting sequences to GenBank
  • DDBJ - DNA Data Bank of Japan

    Protein Structure

  • Microscope 3-D structure database - Hosted by the Biocomputing Unit at the 'Centro Nacional de Biotecnología' (CNB)
  • NRL_3D - Protein structure database

    Other

  • The Genome Database - Supporting the Human Genome Project
  • The Genome Sequence Database - Based at the National Center for Genome Research
  • Group I intron Database
  • HIV sequence database - At Los Alamos
  • Medline Query Form - Medline is an excellent bibliographic database

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    Sequence Searching, and Sequence Retrieval

    The first six links below all use the Sequence Retrieval System (SRS) interface. These sites all allow web based searching and retrieval of nucleotide and protein sequence. They also allow you to query most of the major bioinformatic databases and retrieve textual information. This is by no means a complete list of sites with SRS! Select a site that is nearest to you.

  • Sequence Retrieval System 1 - Based at the Human Genome Mapping Project, Hinxton, UK.
  • Sequence Retrieval System 2 - Another SRS site, this time at the EMBL site in Heidelberg
  • Sequence Retrieval System 3 - This one's at the CSC site in Finland
  • Sequence Retrieval System 4 - BEN, The Belgian EMBnet node
  • Sequence Retrieval System 5 - At the Hungarian EMBnet node
  • Sequence Retrieval System 6 - This one's based at the Weizmann Institute of Science, the Israeli EMBnet node

    In addition to SRS, there are other ways of retrieving sequences and searching for data. Here are a few examples

  • Entrez - Another multipurpose tool for searching and retrieving sequences. Highly reccommended.
  • Genomes Organism Representation - Find out about the genome of the organism of your choice, uses Entrez
  • Bio-wURLd - Search URL's for bio related stuff.
  • Medline Query Form - Search and search again
  • Sequence Alerting System - A great idea. A web site that watches your sequence(s) of interest and emails you when a new homologue appears in the databases.
  • BioTech: Internet Searching Tools - Contains list of yet more places to search

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    General Bioinformatics Web Sites

    Many of these sites will offer the same sorts of links (many to other bioinformatic sites), many will have links to an SRS (see above) or other facilities for sequence retrieval.

    Academic Sites

  • E.B.I. The European Bioinformatics Institute at Cambridge
  • ExPASy - Molecular biology server of the Geneva University Hospital and the University of Geneva
  • Sequence and Structure Analysis - At the Skirbal Institute for Molecular Medicine, New York, USA
  • Mouse Gene Dictionary - Mouse genomic resources
  • Daresbury Laboratory home page - Home to the excellent Seqnet sequence analysis facility
  • Cambridge School of the Biological Sciences - including WU-BLAST 2 server
  • Walter Gilbert's Bioinformatics Group - Based at Harvard.
  • Australian National University Bioinformatics Hypermedia Server - At Canberra
  • BRASS home pageThe Bioinfomatics Resource for Algorithms, Software and Sequences, based at the University of Manchester
  • Southampton Bioinformatics Data Server
  • The CMS Molecular Biology Resource - Featuring a LOT of links
  • The World-Wide Web Virtual Library: Biosciences - containing a lot of links
  • BioMOO, the biologists' virtual meeting place- allows you to interact with your colleagues
  • DerBrowser - A "Genome Navigator" for browsing the yeast, mouse, and human genomes
  • How much of the human genome has been sequenced? - Click to find out!
  • The John Hopkins Bio-Informatics Home Page
  • PEDANT - Protein Extraction, Description, and ANalysis Tool: Lots of information on sequenced genomes
  • Sequence Alerting System - A great idea. A web site that watches your sequence(s) of interest and emails you when a new homologue appears in the databases.

    Corporate/Government Sites

  • EMBL - European Molecular Biology Laboratory
  • N.C.B.I - The National Center for Biotechnology Information, home to the GenBank database
  • TIGR - The Institute for Genomic Research
  • The Jackson Laboratory - Everything you wanted to know about mouse genomics
  • The Sanger Centre - Where they are helping to sequence (amongst other things), the C. elegans genome
  • M.I.P.S. - Munich Information Centre for Protein Sequences, an excellent yeast site
  • Magpie - Containing comprehensive review of various genome sequencing projects

  • The Human Gene Mutation Database

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    Subject Specific Bioinformatics Web Sites

    These sites are more likely to concentrate on a particular area of bioinformatics. These sites are further divided into the various areas of bioinformatics.

    Codon Usage

  • Information on codon usage
  • Fop Home Page - Which refers to Frequency of Optimal Codons
  • CUTG - Codon Usage Tabulated from GenBank
  • Correspondence Analysis of Codon Usage - By one of our former lab members, John Peden.

    Computing, Software, Programming etc.

  • FTP directory listing of GNU - Every bit of UNIX software you'll ever need
  • Bioperl Development List - Perl is an extremely useful programming language
  • TreeView - Site at Glasgow University where you can obtain TreeView Phylogeny software
  • Phylogenetic Analysis Computer Programs - An exhaustive guide to phylogenetic software, including information on how to obtain it

    Correspondence Analysis

  • Automated web-site for correspondance analyis
  • Correspondence Analysis of Codon Usage - By one of our former lab members, John Peden.

    Genome Analysis/Genomic Comparisons

  • PEDANT - Protein Extraction, Description, and ANalysis Tool: Lots of information on sequenced genomes
  • Magpie - Containing comprehensive review of various genome sequencing projects
  • DerBrowser - A "Genome Navigator" for browsing the yeast, mouse, and human genomes
  • TIGR - The Institute for Genomic Research
  • Genomes Organism Representation - Find out about the genome of the organism of your choice, uses Entrez
  • National Center for Genome Resources

    Phylogenetics

  • The Tree of Life Home Page - Useful for tracking down taxonomic classifications
  • NCBI Taxonomy homepage - Much the same as above
  • Introduction to Phylogenetic Biology - A good primer for those that need it
  • Phylogenetic Analysis Computer Programs - An exhaustive guide to phylogenetic software, including information on how to obtain it
  • TreeView - Site at Glasgow University where you can obtain TreeView Phylogeny software

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    Model Organisms

    So many organisms now are being studied at the genomic level, most of them have at least one dedicated web-site as well, if not more. The following is a selection of sites for those organisms with a well characterised genome

    HIV - Human Immunodeficiency Virus

  • HIV sequence database - At Los Alamos
  • National Agency of Research on AIDS - ANRS, based in Marseilles

    Escherichia coli

  • The E.coli Genome Center - at the University of Wisconsin

    Haemophilus influenzae

  • The Haemophilus influenzae Rd Genome Database (HIDB)

    The yeast Saccharomyces cerevisiae

  • The Saccharomyces Genome Database - S.G.D., for every thing you'll ever need to know about yeast
  • M.I.P.S. - Munich Information Centre for Protein Sequences, an excellent yeast site
  • The Yeast Genome Directory - As featured in the Nature special supplement
  • Yeast Genome Navigator
  • YPD - The Yeast Protein Database

    The nematode Caenorhabditis elegans

  • The C. elegans home page - Based at the Sanger Centre
  • ACEDB FTP site

    The mouse

  • Mouse Gene Dictionary - Mouse genomic resources
  • The Jackson Laboratory - Everything you wanted to know about mouse genomics

    The Human Genome Project

  • The Genome Database - Supporting the Human Genome Project
  • The Computational Biology Group and the Human Genome Project at UCSC. Host to a downloadable "working draft" of the human genome, available for download as a full data set or by individual clone contig.

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    Journals

  • Nature
  • Science
  • Molecular Biology and Evolution
  • Nucleic Acids Research
  • Bioinformatics
  • The Journal of Molecular Biology
  • Genetics
  • New Scientist
  • Online Journal of Bioinformatics
  • Internet Science Journal

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