Scientific Literature

• NCBI Entrez - The Life Science Search Engine
    
• NLM Gateway
   
  
• Scirus - by Elsevier, "for scientific information only"

Model organisms

• FlyBase - Drosophila Database
    Genes Refs Stocks People Alleles Aberrations Clones Transposons Insertions Bionet news
• Wormbase - C. elegans Database
    Anything Any Gene Author/Person Allele Cell Clone Database Model Gene Ontology Term Gene Name, 3-letter Gene Name, Cosmid Genetic Map Genbank Accession Number Literature Search Microarray Expression Experiment Operon Primer Pair Protein, Any Protein, C. elegans Protein Family or Motif RNAi Experiment Sequence, Any Sequence, C. elegans Genomic Strain, C. elegans Y2H interaction  
• SaccDB - Yeast Database
    Gene Name Gene Info Clone  Protein Seq. Name  SGDID  Colleague Author Text    

Medical Information

• OMD - Online Medical Dictionary
   

• SLIM - Pubmed focused on clinical articles
• GOPubmed - based on Gene Ontology, GO 
• iHOP - information hyperlinked over proteins
• eTblast - a novel biomedical database search system
• vivisimo - clustered searches, incl. Pubmed
  biometacluster - Velocity for Life Sciences
• chmoogle - chemistry on the web, incl. substructure searching
• MeSH browser - Medical Subject Headings

• DoD2006- Database of Databases
• NIH - US National Institutes of Health
  NCBI - Natl Center for Biotech. Info. - site map, ..
  NLM - Natl Library of Medicine
  SIS - Special Information Svcs (Toxnet, ChemIDPlus)
  
• EBI - European Bioinformatics Institute
• ExPaSy - Expert Protein Analysis System
  Life Science Links - link collection
• GeneCards - Weizman Institute of Science
• Biol.net - extensive and up-to-date collection of links
• IUBMB - intl. union of biochem. and mol. biol. - toc
  biochemistry, enzymes, amino acids, 
• IUPAC - intl. union of pure and applied chemistry - site map,
• CUTG - Codon Usage Database
• wikipedia - free encyclopedia that anyone may contribute

• PredictProtein - @EMBL-Heidelberg
• PROSal protein analysis launcher at SBNet (Sweden)
• EBI, tools and EMBNET.CH, with EXPASY,
• NIH, tools - NLM - NCBI, site-map, tools
• NPSA - Network Protein Sequence Analysis @PBIL, see also PROSCAN
• REBASE - Restriction Enzyme Database
• Webcutter - cut your sequence
• Colorado State University toolkit, dotplot, translate DNA to protein

• NCBI: BLAST
  
• EBI: tools: BLAST2, fasta3, S-W
• EMBNet.CH: BLAST2
• SDSC: MEME and MAST - motif alignment and search tool
• Blast: Tutorial

• EBI: clustalw
• Boxshade -.shading aligned sequences

• Textbook
  • Tree of Life - Phylogeney
  • BioCarta - molecular and cellular pathways
  • KEGG - Kyoto Enzyclopedia of Genes and Genomes
  • Advanced Developmental Biology
  • The Interactive Fly
  • AccessExcellence 
• NCBI Programming Utilities
• NCBI Resource Guide

• Database of Databases - DoD2006
• Genomes
  • ensemble,
• DNA, RNA, EST, nucleic acids
  • NCBI: Genbank, OMIM
  • EMBL - European
  • DDBJ - DNA databank of Japan
  • ESTs - dbEST
• Protein
  • Peptide Atlas.
  • Uniprot, most comprehensive catalog on proteins, created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.
  • Swissprot, find, HPI (Human Protein Initiative)
  • PIR, protein information resource
  • OWL, SWISS-PROT, PIR (1-3), GenBank (translation) and NRL-3D, SWISS-PROT
  • RCSB (research collaboration for Structural Bioiformatics - PDB - 3D Protein databank
• Motifs
  • InterPro (Prosite, Pfam, Prints;Prodom)
  • HITS - SBIs free database of domains
  • Prosite - ExPaSy Database of protein families and domains
  • PATScan -
  • CD-Search (Conserved Domains, NCBI)
  • Smart - Simple Mod. Arch. Res. Tool
  • Pfam - Hidden Markov hmmr
  • PRINTS (combination of motifs)
  • ProDom -
  • PIR - protein information resources
  • NDB: Structure Finder 
  • Heidelberg: Predict protein
  • big-PI predictor by B. Eisenhaber, IMP, Vienna
  • TESS -
  • promoterscan on zeon -
  • Signalscan -
  • Repeat masker -
  • genscan - MIT, identification of complete gene structures in genomic DNA
  • UTRScan - collection of functional sequence patterns located in 5' or 3' UTR sequences.
  • CpG islands: Pasteur