Web resources for bioinformatics
The following list of web resources was compiled by Prof. Bill Noble. If you find dead links, please contact me (firstname.lastname@example.org) and I will try to track down the correct URL.
Genomics and bioinformatics centers
- National Center for Biotechnology Information home page
- Computational Molecular Biology at NIH
- European Moloecular Biology Laboratory WWW services
- European Bioinformatics Institute home page
- Sanger Centre home page
- Protein Bata Bank (PDB)
Indexes of bioinformatic tools and genomics projects
DNA analysis tools
- Gene Finding Format (GFF) tools and definition
- C. elegans genes in GFF format (from 1998 Science paper)
- Berkeley's Drosophila genome genefinding experiment (Look down the page a bit for the link. Contains tutorial, data, results comparing different genefinders)
- Banbury cross genefinding benchmark data and international genefinding program results (now a bit out of date)
- UCSC GENIE genefinding program
- HMMgene genefinding program
- GRAIL genefinding program
- GenScan genefinding program
- PROCRUSTES genefinding program
- University of Wash. Genome Center RepeatMasker page
- Ewan Birney's Genewise package. HMMs for protein, EST and genomic DNA analysis.
- Computational genefinding tutorial
Protein analysis tools
- UCSC SAM-T98 (-T99) HMM applications server
- UCSC SAM Hidden Markov Modeling program
- Sean Eddy's HMMer Hidden Markov modeling program
- SWISSPROT database
- PFAM database HMMs for protein families.
- SMART database HMMs for protein families.
- BLOCKS database Database of protein motifs.
- UCLA/DOE protein structure prediction program
- CASP protein structure prediction contest home page
- Frontiers of Protein Structure Prediction (comparative analysis)
- RASMOL and CHIME protein structure viewers
- CATH database of protein structure classification
- FSSP database of protein structure classification
- SCOP database of protein structure classification (see also temp address of new version of SCOP database of protein structure classification
- PHD. Prediction of protein secondary structure.
- AAindex. Databases of amino acid properties.
Home pages for other bioinformatics courses
- Mark Craven: Bioinformatics
- Kevin Karplus: Computational Biology
- David Haussler: Computational Biology
- Georg Fuellen: Full on-line Hypertext Biocomputing
- States/Zuker/Eddy/Gish: Computational Molecular Biology (This course contains web pages to help students unfamiliar with UNIX and Perl get started.)
- Karp/Ruzzo/Tompa: Algorithms in Molecular Biology (Includes slides from all lectures.)
- Naor/Shamir: Algorithms for Moloecular Biology (Includes notes taken by student "scribes" from lectures.)
- Altman/Brutlag/Levitt: Algorithms and Representations for Molecular Biology (Includes lots of resources and lectures.)
- Mike Levitt: Computational Structural Biology: Protein Simulation and Structure Prediction
- Doug Brutlag: Computer Applications in Molecular Biology
- Steven Salzberg: Computational Biology
- Rik Belew: Computational Biology
- ISCB's listing of on-line bioinformatics courses
Academic programs in bioinformatics/biotech at other institutions
- Center for Computational and Experimental Genomics, USC
- BioMolecular Engineering Research Center, Boston U.
- Dept. of Molecular Biotechnology, University of Washington
- Medical Informatics at Stanford
- Computational Molecular Biology Program at Washington Univ.
- Keck Center for Advanced Training in Computational Biology (University of Pittsburgh and Carnegie Mellon, and also Baylor, Rice and the University of Houston)
- Computational Biology and Informatics Program at U. Penn.
- Bioinformatics and Computational Biology Ph.D. Program at George Mason
- MIT Whitehead Center for Genome Research
- Berkeley-UCSF joint program in bioengineering
- ISCB's list of academic programs in Computational Biology
Bibliographies for bioinformatics literature and on-line primers
- DOE: Nice on-line primer on molecular genetics and human genome project with figures
- DOE: Glossary of molecular biology and genome informatics terms
- DOE: Home page for the Human Genome Project
- On-line primer on DNA structure
- On-line protein structure tutorial (requires free CHIME plugin)
- Computational genefinding tutorial
- Burkhard Rost review paper on protein structure prediction
- Index to on-line and regular journals in the biosciences
- Bioinformatics Journal
- Journal of Computational Biology
- Extensive bibliography of papers on computational genefinding
- Naor/Shamir: class page containing several bibliographies