Genomics and Bioinformatics Centers

• National Center for Biotechnology Information home page
  • NCBI's ENTREZ browser for biosequence databases
  • NCBI's BLAST biosequence database search tool
• Computational Molecular Biology at NIH
• European Moloecular Biology Laboratory WWW services
  • EMBL's SRS browser for biosequence databases
  • EMBL's PHD program to predict protein secondary structure
• European Bioinformatics Institute home page
• Sanger Centre home page
• Protein Bata Bank (PDB)

Indexes of Bioinformatic tools and genomics projects

• Pedro's page: a list of URLs for many sequence analysis programs
• BioCatalog: EBI's page listing sequence analysis programs worldwide
• DOE's Genome Channel
• List of current Genome Sequencing 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• Banbury cross genefinding benchmark data and international genefinding program results (now a bit out of date)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
• MOLMOL
• PHD. Prediction of protein secondary structure.
• AAindex. Databases of amino acid properties.

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