Bioinformatics Resources

List has been adapted from World of Bioinformatics Links as well as other online resources.

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

    Click     here to go to top of page.

    Sequence Searching, and Sequence Retrieval  

  • Entrez - Another multipurpose tool for searching and retrieving sequences.
  • 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

    Click     here to go to top of page.

    General Bioinformatics Web Sites

    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

    Click     here to go to top of page.

    Subject Specific Bioinformatics Web Sites

    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

    Click     here to go to top of page.


  • 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

    • Copyright Louis Licamele 2010