1. databases
   1. generalized DNA, protein, and carbohydrate databases
      1. primary sequence databases
         1. EMBL
         2. GeneBank
         3. DDBJ
      2. protein sequence databases
         1. SWISS-PROT
         2. TrEMBL
         3. PIR-PSD
         4. uniProt
         5. UniRef
         6. IPI
      3. Carbohydrate databases
         1. CarbBank
      4. 3D structure databses
         1. PDB
         2. EBI-MSD
         3. NDB
   2. specialized databases
      1. specialized sequence
         1. dbEST
         2. TGI
         3. Mendel ESTs
         4. Bodymanp
         5. dbGSS
         6. dbSNP
         7. SNPer
         8. dbSTS
         9. HGVBASE
      2. RNA databases
         1. ssu and lsu rRNA database
         2. RDP
         3. miRNA Registry
      3. genome databases
         1. collections
            1. GOLD
            2. Genomes at NCBI
            3. Organism Specific Databases
            4. Microbial Genomes
            5. PEDANT
            6. Ensembl
            7. GeneQuiz
            8. HAMAP
            9. UK CropNet
            10. ArkDb
            11. MITOP
            12. Codon Usage Database
            13. Gene Census
         2. model organism databases
            1. E.coli
            2. E. coli Genome Center
            3. The E. coli index
            4. S. oerevisiae (Baker's yeast)
            5. SGD
            6. CYGD
            7. Arabidopsis thaliana
            8. MATDB
            9. TAIR
            10. KAOS
            11. Arabidopsis Genome Analysis
            12. TIGR Arabidopsis thaliana datbase
            13. Oryza sativa (Rice)
            14. RGP
            15. Granebe
            16. INE
            17. Caenorhabditis elegans
            18. WormBase
            19. Drosophila melanogaster (Fruit fly)
            20. FLYBase
            21. BDGP
            22. Danio rerio (Zebrafish)
            23. ZFIN
            24. WashU-Zebrafish Genome Resources
            25. Mus musculus (Mouse)
            26. MGI
            27. Homo sapiens
            28. GDB
            29. HIB
            30. Human genome resources
            31. Human genome browser
            32. HGP
            33. GeneLinkes
      4. specialized protein databases
         1. proteome databases
            1. Proteome analysis
         2. specific protein fanily databse
            1. Proweb
            2. TRANSFAC
            3. GPCRDB
            4. PKR
            5. ENZYME
            6. MEROPS
            7. Prolysis
            8. CAZy
            9. PROMISE
            10. ReLiBase
            11. IMGT
            12. REBASE
         3. protein classification database
            1. CluSTr
            2. Pfam
            3. TIGRFAMs
            4. Hits
            5. SCOP
            6. CATH
            7. BioSpace
            8. LPFC
            9. Dali
            10. ENZYME
            11. Enzyme Structures Database
            12. PRESAGE
            13. CDD
         4. specialized structure database
            1. Protein-Nucleic Acid Recognition Database
            2. 3DInSight
            3. MolMovDB
         5. pathway database
            1. KEGG
            2. LIGAND
            3. BRITE
            4. Boehringer Mannheim - Biochemical pathways
            5. BioCyc
            6. WIT
            7. EMP
            8. UM-BBD
            9. BRENDA
            10. SRS
         6. Microarray database
            1. ArrayExpress
            2. GEO
         7. 2D-page database
            1. Gelbank
            2. Swiss-2DPAGE
2. database search
   1. text-based
      1. ENTREZ
      2. SRS
      3. DBGET/LinkDB
      4. SSS
      5. Molecules R US
      6. MIA
   2. sequences-based
      1. BLAST
      2. FASTA
      3. MPsrch
      4. BLAST Microbial Genomes
      5. Genome and proteome FASTA
      6. PIR-NPL3D
   3. motif-based
      1. Kangaroo
      2. ScanProsite
      3. ShapeSifter
   4. structure-based
      1. Search_SCOP
      2. VAST
      3. DALI
      4. Finding 3D Similarity by CE
      5. LIBRA
   5. mass-based protein search
      1. ProteinProspector
      2. PeptIdent
      3. Prowl
      4. Mascot
      5. MassSearch
      6. Mowse
      7. PeptideSearch
      8. Lutefisk
3. analysis tools
   1. DNA sequence analysis tools
      1. Restriction; Detect repeats and unusual patterns
         1. Restrictionmapper
         2. Webcutter
         3. RepeatMasker
         4. REPuter
         5. dnadot
         6. Blast 2 Sequences
         7. LALIGN
      2. Align sequences
         1. Align
         2. MAP
         3. ClustalW
         4. Launcher: multiple alignment
         5. AMAS
         6. CINEMA
      3. Find genes
         1. Sixframe
         2. ORF Finder
         3. GeneMark
         4. GenLang
         5. GeneMachine
         6. NetPlantGene
         7. AAT
      4. Find transcriptional elements
         1. Identification of Prokaryotic/Eukaryotic Promoters
         2. SignalScan
         3. IHF Site/Sigma 54 Promoter searches
         4. FirstEF
      5. Find tRNA
         1. tRNAscan-SE
         2. FAStRNA
      6. Other tools
         1. CountCodon
         2. MAR-Wiz
         3. Reverse Complement
         4. DNA folding server
         5. PRIDE
         6. Netprimer
         7. PCR primer selection
         8. Primer3
         9. GeneFisher
         10. CODEHOP
   2. RNA analysis tools
      1. RNA Fold
      2. RNA World
   3. protein sequence and structure analysis tools
      1. Physicochemical properties
         1. ProtParam
         2. ProTherm
      2. Analyse primary sequence
         1. ProtColourer
         2. ProtScale
         3. SAPS
         4. SignalP
         5. TargetP
         6. PSort
         7. NetOGlyc
         8. DGPI
         9. NetPhos
         10. Scansite
         11. Helical Wheel
         12. Other primary sequence analysis tools at ExPaSy
      3. Alignment
         1. Pairwise
            1. Blast 2 Sequences
            2. SIM
            3. Pairwise sequence alignment
            4. Align
         2. Multiple
            1. ClustalW
            2. MAP
            3. Multiple sequence alignment
            4. AMAS
         3. Editors
            1. CINEMA
            2. BOXSHADE
      4. Predict secondary structure
         1. TMpred
         2. TMHMM
         3. SOSUI
         4. PSort
         5. DAS
         6. HMMTOP
         7. TOPPred2
         8. PredictProtein
         9. JPred
         10. HNN
         11. PSIpred
         12. nnPredict
         13. Other secondary structure prediction tools at ExPASy
         14. BTPRED
         15. Coils
         16. PairCoil
         17. MultiCoil
         18. TOPS
      5. Analyse and model 3D structure
         1. 3D viewers
            1. RasMol
            2. Swiss-Pdb Viewer (Deep View)
            3. Chime
            4. Cn3D
            5. WebMol
         2. 3D analysis
            1. TOPS
            2. DOMPLOT
            3. OCA
            4. STRUCTURE
            5. PsiPred
            6. Predicting Protein 3D structure based on homologous sequence search
            7. LOCK
            8. CE
            9. DALI
            10. LIBRA
            11. VAST
            12. ASC
            13. MolSurfer
            14. Protein-Protein Interaction Server
         3. 3D homology modeling
            1. CPHmodels
            2. Swiss-Model
            3. 3DCrunch
            4. FAMS
            5. 3D-Jigsaw
            6. SDSC1
            7. Meta PP
   4. tools for protein function assignment
      1. Scan or search for patterns, motifs, profiles, domains, families
         1. ScanProsite
         2. PROSCAN
         3. PPSearch
         4. PFSCAN
         5. FingerPRINTScan
         6. BLOCKS Search
         7. eMOTIF-Scan
         8. Scansite
         9. MEME
         10. eMotif-maker
         11. Meta-MEME
         12. CDART
         13. SearchPfam at Wustl
         14. InterProScan
         15. CD-Search
         16. COGnitor
         17. iProClass Search
         18. SMART
         19. PROCAT
         20. ConSurf
         21. ProDom
         22. Modules
         23. SBASE
         24. HSSP
         25. 3Motif
         26. eMATRIX Search
         27. GeneQuiz
      2. Search, computation and analysis of pathways
         1. KEGG
         2. aMAZE
      3. Protein-protein interactions
         1. DIP
         2. PreBIND
         3. BIND
         4. BINDBLAST
         5. MINT
         6. GRID
         7. PPI viewer
         8. STRING
         9. InterPrets
      4. Protein Annotation
         1. PAA
         2. AAT
         3. Artemis
         4. Gene Ontology tools
      5. Automatic alert for related new sequence
         1. PubCrawler
         2. Swiss-Shop
         3. New microbial Genomes Notification
   5. phylogeny
      1. Multiple sequence alignment
         1. ClustalW
         2. Multiple sequence alignment
         3. AMAS
         4. BOXSHADE
         5. Entrez-PopSet
         6. ConSurf
         7. ...more than 100 programs
      2. Organism classification
         1. NCBI Taxonomy
         2. The Tree of Life Project
         3. TreeBASE
   6. microarray analysis tools
      1. ArrayExpress
      2. GEO
      3. SMD
      4. YMD
      5. Expression Profiler
      6. GenMapp
      7. TBI Expression Analysis
      8. other
4. miscellaneous
   1. literature search
      1. PubMed
      2. PubMed Central
      3. FreeMedicalJournals
      4. PubCrawler
   2. patent search
      1. esp@cenet
      2. USPTO
      3. DPD
   3. bioinformatics centers and severs
      1. ANGIS (Australian National Genomic Information Service)
      2. BEN (Belgian EMBNet Node)
      3. Brutlag Bioinformatics Group (at Stanford University, USA)
      4. CBS (Center for Biological Sequence analysis, Denmark)
      5. CIB (Center for Information Biology, Mishima, Jp)
      6. EBI (European Bioinformatics Institute, Hinxton, UK)
      7. EMBnet and related WWW servers
      8. ExPASy (Geneva, CH)
      9. Genestream (at IGH, Montpellier, Fr)
      10. GenomeNet Japan
      11. ISCB (International Society for Computational Biology)
      12. ISREC (Swiss Institute for Experimental Cancer Research)
      13. MBCR (Biomedical Computing Facility)
      14. MIPS (Munich Information Centre for Protein Sequences, Munich, Germ.)
      15. NCBI (National Center for Biotechnology Information, Bethesda MD, USA)
      16. NCGR (National Center for Genome Resources, Santa Fe, New Mexico, USA)
      17. RFCGR (MRC Rosalind Franklin Centre for Genomic Research, Hinxton, UK)
      18. Roslin Institute Bioinformatics (Edinburg, UK)
      19. Sanger Institute (Hinxton, UK)SBG (Structural Bioinformatics Group at the EMBL, Heidelberg, Germany)
      20. SDSC (San Diego Supercomputer Center, USA)
      21. SHGC (Stanford Human Genome Center)
      22. SIB (Swiss Institute for Bioinformatics, Geneva, CH)
      23. Stanford Genome Technology Center
      24. Stanford Genomic Resources
      25. TIGR (The Institute for Genomic Research, USA)
      26. UCL Biochemistry BSM Group (Biomolecular Structure and Modelling Group, UK)
      27. Washington Genome Sequencing Center
   4. medical resources
      1. OMIA
      2. OMIM
      3. The MERCK Manual of Diagnosis and Therapy
   5. protocols
      1. Protocol Online
      2. Molecular Biology Protocols
   6. software
      1. BioCatalog
      2. Logiciels
      3. Molscript
      4. NCBI Toolbox
      5. Phylogeny Programs
      6. BioPerl