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Nucleic Acids Res by wulinqing

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									Supplementary Table 1. NAR Molecular Biology Database Collection: 2008 updatea

Nob    Database namec         Full name and/or description                                     URL
       1. Nucleotide Sequence Databases
       1.1. International Nucleotide Sequence Database Collaboration
 1     DDBJ - DNA Data Bank   All known nucleotide and protein sequences                       http://www.ddbj.nig.ac.jp
       of Japan
 2     EMBL Nucleotide        All known nucleotide and protein sequences                       http://www.ebi.ac.uk/embl.html
       Sequence Database
                ®
 3     GenBank                All known nucleotide and protein sequences                       http://www.ncbi.nlm.nih.gov/Entrez
       1.2. Coding and coding DNA: genes, motifs and regulatory sites
403    ACLAME                 A classification of genetic mobile elements                      http://aclame.ulb.ac.be/
337    CORG                   Comparative Regulatory Genomics: conserved non-coding blocks     http://corg.molgen.mpg.de
                              in vertebrate species
 30    CUTG                   Codon Usage Tabulated from GenBank                               http://www.kazusa.or.jp/codon/
1157   ECRbase                Database of Evolutionary Conserved Regions, promoters, and       http://ecrbase.dcode.org/
                              transcription factor binding sites
668    Entrez Gene            Gene-centered information at NCBI                                http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gen
                                                                                               e
669    FESD                   Functional Element SNPs Database: SNPs located within            http://sysbio.kribb.re.kr/FESD/
                              promoters, UTRs, etc., of human genes
468    FREP                   Functional Repeats in mouse cDNAs                                http://facts.gsc.riken.go.jp/FREP/
480    Genetic Codes          Genetic codes in various organisms and organelles                http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.c
                                                                                               gi?mode=c
1079   GISSD                  Group I Intron Sequence and Structure Database                   http://www.rna.whu.edu.cn/gissd
1083   GyDB                   Gypsy database of mobile genetic elements                        http://gydb.uv.es/gydb/intro.htm
 825   HumHot                 Human meiotic recombination hot spots                            http://www.jncasr.ac.in/humhot/
 932   InSatDb                Sequences and properties of insect microsatellites               http://www.cdfd.org.in/insatdb
 832   ISfinder               Insertion sequences from bacteria and archaea                    http://www-is.biotoul.fr
 512   Islander               Pathogenicity islands and prophages in bacterial genomes         http://www.indiana.edu/~islander
 697   L1Base                 Functional annotation and prediction of LINE-1 elements          http://line1.molgen.mpg.de
  19   MethDB                 DNA methylation data, patterns and profiles                      http://www.methdb.de
 343   MICdb                  Prokaryotic microsatellites                                      http://210.212.212.7/MIC/index.html
 707   NPRD                   Nucleosome Positioning Region Database                           http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?page+
                                                                                               LibInfo+-id+2Xnp11RCiPU+-lib+NUCLEOSOME
931    OriDB                  DNA Replication Origin Database: Confirmed and predicted sites   http://www.oridb.org/
 551   PACRAT                 Archaeal and bacterial intergenic sequence features              No longer maintained
 608   PANDIT                 Protein and associated nucleotide domains with inferred trees    http://www.ebi.ac.uk/goldman-srv/pandit/
 933   Patome                 Annotated sequences from patents and patent applications         http://www.patome.org
 958   PolymiRTS              Polymorphism in microRNA Target Site                             http://compbio.utmem.edu/miRSNP/
1007   PseudoGene.org         Pseudogenes in eukaryotic and prokaryotic genomes                http://www.pseudogene.org/
  21   RECODE                 Genes using programmed translational recoding in their           http://recode.genetics.utah.edu
                              expression
391    RefSeq                 Reference Sequence database: an integrated, non-redundant set    http://www.ncbi.nlm.nih.gov/RefSeq/
                              of genomic DNA, RNA, and protein sequences
1019   RetrOryza              LTR-retrotransposons in rice                                     http://www.retroryza.org
 309   S/MARt DB              Nuclear scaffold/matrix attached regions                         http://smartdb.bioinf.med.uni-goettingen.de/
1013   SNPSTR                 Microsatellite compound markers in 5 vertebrate genomes          http://www3.imperial.ac.uk/theoreticalgenomics/data-
                                                                                               software
  47   STRBase                Short tandem DNA repeats database                                http://www.cstl.nist.gov/div831/strbase/
 929   Synthetic Gene DB      Synthetic genes described in peer-reviewed literature            http://www.evolvingcode.net/codon/sgdb/index.php
 588   TIGR plant repeat DB   Classification of repetitive sequences in plant genomes          http://www.tigr.org/tdb/e2k1/plant.repeats
1141   TranspoGene            Transposed elements influence on the transcriptome of seven      http://transpogene.tau.ac.il/
                              vertebrates and invertebrates
1035   TRDB                   Tandem repeats in genomic DNA                                    http://tandem.bu.edu/cgi-bin/trdb/trdb.exe
1143   UgMicroSatdb           UniGene MicroSatellite database: short tandem repeats from       http://ipu.ac.in/usbt/UgMicroSatdb.htm
                              various eukaryotic genomes
320    UniVec                 Vector sequences, adapters, linkers and primers used in DNA      http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html
                              cloning, used to check for vector contamination
 252   UTRdb/UTRsite          5'- and 3'-UTRs of eukaryotic mRNAs                              http://bighost.area.ba.cnr.it/BIG/UTRHome/
1146   UTRome                 3'UTRs and their functional elements in C. elegans               http://www.utrome.org
 302   Vectordb               Characterization and classification of nucleic acid vectors      http://seq.yeastgenome.org/vectordb/
 968   VISTA Enhancer         Enhancer elements in the human genome                            http://enhancer.lbl.gov/
       Browser
       1.3. Gene structure, introns and exons, splice sites
414    ASAP II                Comparative analysis of alternative splicing in animal species   http://bioinfo.mbi.ucla.edu/ASAP2/
 10    ASDB                   Alternative Splicing Database: protein products and expression   http://hazelton.lbl.gov/~teplitski/alt/
                              patterns of alternatively-spliced genes
639    ASHESdb                Alternatively Spliced Human genes by Exon Skipping               http://sege.ntu.edu.sg/wester/ashes/
 28    ASTD                   Alternative Splicing and Transcript Diversity database           http://www.ebi.ac.uk/astd/
920    ATD                    Alternate transcript diversity database                          Superseded by ASTD, no. 28
803    ChimerDB               Chimeric (fusion) sequences in human, rat and mouse              http://genome.ewha.ac.kr/ChimerDB/
450    EASED                  Extended Alternatively Spliced EST Database                      http://eased.bioinf.mdc-berlin.de/
667    ECgene                 Genome annotation for alternative splicing                       http://genome.ewha.ac.kr/ECgene/
631    EDAS                   EST-derived alternative splicing database                        http://www.ig-msk.ru:8005/EDAS/
 32    EID                     Exon-intron database                                                 http://www.meduohio.edu/bioinfo/eid/
 34    ExInt                   Exon–intron structure of eukaryotic genes                            http://sege.ntu.edu.sg/wester/exint/
913    ExtraTRAIN              Extragenic regions and transcriptional regulators in bacteria and    http://www.era7.com/ExtraTrain/
                               archaea
782    FUGOID                  Functional genomics of organelle introns database                    http://web.austin.utexas.edu/fugoid/introndata/main.ht
                                                                                                    m
 970   H-DBAS                  Human database of alternative splicing                               http://jbirc.jbic.or.jp/h-dbas/
 821   Hollywood               Exon annotation database                                             http://hollywood.mit.edu
           3
  36   HS D                    Homo Sapiens Splice Sites Dataset                                    http://www.sci.unisannio.it/docenti/rampone/
 238   Intronerator            Alternative splicing in C. elegans and C. briggsae                   http://hgwdev-hiram.cse.ucsc.edu/IntronWS120/
1122   ProSAS                  Protein Structure and Alternative Splicing: effects of alternative   http://services.bio.ifi.lmu.de/ProSAS
                               splicing events on protein structure
46     SpliceDB                Canonical and non-canonical mammalian splice sites                   http://www.softberry.com/berry.phtml?topic=splicedb&
                                                                                                    group=data&subgroup=spldb
746    SpliceInfo              Modes of alternative splicing in human genome                        http://spliceinfo.mbc.nctu.edu.tw/
580    SpliceNest              Visualizing Splicing of Genes from EST Data                          http://splicenest.molgen.mpg.de/
927    TassDB                  TAndem Splice Site Database                                          http://helios.informatik.uni-freiburg.de/TassDB/
937    U12DB                   Database of orthologous U12-type spliceosomal introns                http://genome.imim.es/cgi-bin/u12db/u12db.cgi
305    Xpro                    Eukaryotic protein-encoding DNA sequences, both intron-              http://origin.bic.nus.edu.sg/xpro/
                               containing and intron-less genes
342    Yeast Intron Database   Ares lab database of splicesomal introns in S. cerevisiae            http://www.cse.ucsc.edu/research/compbio/yeast_intro
                                                                                                    ns.html
       1.4. Transcriptional regulator sites and transcription factors
 795   ABS                     Annotated regulatory binding sites from orthologous promoters        http://genome.imim.es/datasets/abs2005/
 231   ACTIVITY                Functional DNA/RNA site activity                                     http://wwwmgs.bionet.nsc.ru/mgs/systems/activity/
 308   ASPD                    Artificial selected proteins/peptides database                       http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/
 805   CisRed                  Human regulatory DNA sequence motifs                                 http://www.cisred.org/
1058   CMGSDB                  Computational models for gene silencing in C. elegans                https://bioinformatics.cs.vt.edu/cmgs/CMGSDB/
1062   COXPRESdb               Coexpressed genes and networks in human and mouse                    http://coxpresdb.hgc.jp/
1063   CTCF Binding Site DB    Experimentally identified and predicted CTCF binding sties           http://insulatordb.utmem.edu/
 807   DBD                     Transcription factor prediction database                             http://www.transcriptionfactor.org/
  31   DBTBS                   Bacillus subtilis promoters and transcription factors                http://dbtbs.hgc.jp/
 591   DBTSS                   Database of transcriptional start sites                              http://dbtss.hgc.jp/
 663   DoOP                    Databases of Orthologous Promoters: chordates and plants             http://doop.abc.hu/
 106   DPInteract              Binding sites for E. coli DNA-binding proteins                       http://arep.med.harvard.edu/dpinteract/
  33   EPD                     Eukaryotic promoter database                                         http://www.epd.isb-sib.ch/
 329   GeneNet                 Database on gene network components                                  http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet/
1036   GenomeTraFaC            Conserved regulatory elements of human and mouse genes               http://genometrafac.cchmc.org
 823   HTPSELEX                Transcription factor binding site sequences obtained using high-     http://www.isrec.isb-sib.ch/htpselex/
                           throughput SELEX method
 516   JASPAR              PSSMs for transcription factor DNA-binding sites                         http://jaspar.cgb.ki.se
 700   MAPPER              Putative transcription factor binding sites in various genomes           http://bio.chip.org/mapper
 842   MPromDB             Mammalian promoter database                                              http://bioinformatics.med.ohio-state.edu/MPromDb
 846   ODB                 Operon database                                                          http://odb.kuicr.kyoto-u.ac.jp/
 185   ooTFD               Object-oriented transcription factors database                           http://www.ifti.org/ootfd
1107   ORegAnno            Open REGulatory ANNOtation database                                      http://www.oreganno.org/
 711   Osteo-Promoter DB   Genes in osteogenic proliferation and differentiation                    http://www.opd.tau.ac.il
  40   PLACE               Plant cis-acting regulatory DNA elements                                 http://www.dna.affrc.go.jp/PLACE/
  41   PlantCARE           Plant promoters and cis-acting regulatory elements                       http://bioinformatics.psb.ugent.be/webtools/plantcare/h
                                                                                                    tml/
563    PlantProm           Plant promoter sequences for RNA polymerase II                           http://mendel.cs.rhul.ac.uk/mendel.php?topic=plantpro
                                                                                                    m
1117   PlantTFDB           Plant Transcription Factor Database                                      http://planttfdb.cbi.pku.edu.cn
1005   PReMod              Predicted transcriptional regulatory modules in the human genome         http://genomequebec.mcgill.ca/PReMod
 566   PRODORIC            Prokaryotic database of gene regulation networks                         http://prodoric.tu-bs.de/
  42   PromEC              E. coli promoters with experimentally-identified transcriptional start   http://margalit.huji.ac.il/promec/
                           sites
1123   ProTISA             Translation Initiation Site Annotation in prokaryotic genomes            http://mech.ctb.pku.edu.cn/protisa/
 116   RegulonDB           Transcriptional regulation and operon organization in E.coli             http://regulondb.ccg.unam.mx/
  45   rSNP Guide          SNPs in regulatory gene regions                                          http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/
 577   SCPD                Saccharomyces cerevisiae promoter database                               http://rulai.cshl.edu/SCPD/
 246   SELEXdb             Selected DNA/RNA functional site sequences                               http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/
1015   SwissRegulon        Genome-wide annotations of regulatory sites in the intergenic            http://www.swissregulon.unibas.ch
       database            regions
227    TESS                Transcription element search system                                      http://www.cbil.upenn.edu/tess
904    TiProD              Tissue-specific promoter database                                        http://tiprod.cbi.pku.edu.cn:8080/index.html
756    Tractor_DB          Transcription factors in gamma-proteobacteria database                   http://www.tractor.lncc.br
                    ®
345    TRANSCompel         Transcriptional regulation, composite regulatory elements                http://www.gene-regulation.com/pub/
                                                                                                    databases.html#transcompel
                   ®
 340   TRANSFAC            Transcription factors, gene regulation, positional weight matrices       http://www.gene-regulation.com
1141   TransfactomeDB      Nucleotide sequence specificity and condition-specific regulatory        http://bussemakerlab.org/YeastTransfactomeDB/
                           activity of trans-acting factors
341    TRANSPATH           Signal transduction pathways, vizualization and expression data          http://www.biobase.de/pages/products/databases.html
                           analysis
 48    Transterm           Codon usage, start and stop signals                                      http://guinevere.otago.ac.nz/transterm.html
757    TRED                Transcriptional regulatory element database                              http://rulai.cshl.edu/tred
 49    TRRD                Transcription regulatory regions of eukaryotic genes                     http://www.bionet.nsc.ru/trrd/
314    TrSDB               Transcription factor database                                            http://bioinf.uab.es/cgi-bin/trsdb/trsdb.pl
792    YEASTRACT           Yeast transcriptional regulation                                         http://www.yeastract.com
       2. RNA Sequence, Structure and Functions
229    16S and 23S rRNA          16S and 23S ribosomal RNA mutations                                 http://ribosome.fandm.edu
       Mutation Database
1041   3D rRNA modification      Locations of modified rRNA nucleotides within the 3D structure of   http://people.biochem.umass.edu/fournierlab/3dmodm
       maps                      the ribosome                                                        ap/
 230   5S rRNA Database          5S rRNA sequences                                                   http://biobases.ibch.poznan.pl/5SData/
 411   Aptamer Database          Small RNA/DNA molecules binding nucleic acids, proteins             http://aptamer.icmb.utexas.edu
 232   ARED                       AU-rich element-containing mRNAs                                   http://brp.kfshrc.edu.sa/ARED
 797   Argonaute                 Gene regulation by mammalian microRNAs                              http://argonaute.uni-hd.de
 984   dbRES                     Database of known RNA editing sites                                 http://bioinfo.au.tsinghua.edu.cn/dbRES/
 463   European rRNA DB          All complete or nearly complete rRNA sequences                      http://www.psb.ugent.be/rRNA/
1027   fRNAdb                    Functional RNA Database: noncoding transcripts that affect gene     http://www.ncrna.org/
                                 expression
878    Greengenes                Multiple sequence alignment of prokaryotic 16S rDNA                 http://greengenes.llnl.gov/16S/
820    GRSDB                     G-rich sequences database                                           http://bioinformatics.ramapo.edu/GRSDB2/
490    G-tRNA-db                 Genomic tRNA Database                                               http://lowelab.ucsc.edu/GtRNAdb/
236    Guide RNA Database                                                                            No longer maintained
 76    HIV Sequence DB           HIV RNA sequences                                                   http://hiv-web.lanl.gov/
689    HuSiDa                    Human siRNA database                                                http://itb.biologie.hu-
                                                                                                     berlin.de/~nebulus/sirna/index.htm
 237   HyPaLib                   Hybrid pattern library: structural elements in classes of RNA       Not actively maintained
 379   IRESdb -                  the Internal Ribosome Entry Site database                           http://ifr31w3.toulouse.inserm.fr/IRESdatabase/
 831   IRESite                   Experimentally studied internal ribosome entry sites                http://www.iresite.org
 838   MeRNA                     Metal ion binding sites in RNA                                      http://merna.lbl.gov
1097   microRNA.org              microRNA target predictions and expression profiles                 http://www.microrna.org
 529   miRBase                   MicroRNA sequences, names, and predicted targets in animals         http://microrna.sanger.ac.uk/sequences/
1098   miRGator                  microRNA target prediction, functional analysis, and gene           http://genome.ewha.ac.kr/miRGator/miRGator.html
                                 expression data
994    miRGen                    Animal microRNAs located in introns, exons, UTRs, pseudogenes       http://www.diana.pcbi.upenn.edu/miRGen
                                 and CpG islands
895    miRNAMap                  microRNA precursors and their mapping to targets in vertebrate      http://mirnamap.mbc.nctu.edu.tw
                                 genomes
378    Mobile group II introns   Database for mobile group II introns                                http://www.fp.ucalgary.ca/group2introns/
840    MODOMICS                  Database of RNA modification pathways                               http://genesilico.pl/modomics/
997    NATsDB                    Natural Antisense Transcripts database                              http://nats.cbi.pku.edu.cn
380    NCIR                      Non-Canonical Interactions in RNA                                   http://prion.bchs.uh.edu/bp_type/
381    ncRNAs database           Non-coding RNAs with regulatory functions                           http://biobases.ibch.poznan.pl/ncRNA/
705    NONCODE                   Database of noncoding RNAs                                          http://bioinfo.ibp.ac.cn/NONCODE/index.htm
845    NPInter                   Noncoding RNA-protein interactions                                  http://bioinfo.ibp.ac.cn/NPInter/index.php
1114   piRNABank               Sequences and properties of Piwi-interacting RNAs (piRNAs) in   http://pirnabank.ibab.ac.in/
                               human, mouse and rat
 564   Plant snoRNA DB         snoRNA genes in plant species                                   http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home
 240   PLANTncRNAs                                                                             No longer maintained
 241   PLMItRNA                Mitochondrial tRNA genes in photosynthetic eukaryotes           http://bighost.area.ba.cnr.it/PLMItRNA/
 723   PolyA_DB                Database of mammalian mRNA polyadenylation                      http://polya.umdnj.edu/
 242   PseudoBase              Database of RNA pseudoknots                                     http://wwwbio.leidenuniv.nl/~Batenburg/PKB.html
1009   REDIdb                  An RNA editing database                                         http://biologia.unical.it/py_script/search.html
 382   Rfam                    Non-coding RNA families                                         http://www.sanger.ac.uk/Software/Rfam/
 243   RDP-II                  Ribosomal Database Project                                      http://rdp.cme.msu.edu
 244   RISSC                   Ribosomal Internal Spacer Sequence Collection                   http://egg.umh.es/rissc
 245   RNA Modification DB     Naturally modified nucleosides in RNA                           http://medlib.med.utah.edu/RNAmods/
 900   RNA SSTRAND             RNA secondary structure data and structural motifs              http://www.rnasoft.ca/sstrand
 630   RNAdb                   Mammalian noncoding RNA database                                http://ncrna.bioinformatics.com.au
 862   RNAi codex              Clones from mouse, human and rat shRNA libraries                http://codex.cshl.org
1162   siRecords               Experimentally tested mammalian siRNAs                          http://sirecords.umn.edu/siRecords/
 629   siRNAdb                 Functional human siRNA sequences                                http://sirna.cgb.ki.se
 247   Small RNA Database                                                                      No longer maintained
 869   snoRNA-LBME-db          Human snoRNAs and Cajal body-specific RNAs (scaRNAs)            http://www-snorna.biotoul.fr/
 962   Sno/scaRNAbase          Small nucleolar RNAs and cajal body-specific RNAs               http://gene.fudan.sh.cn/snoRNAbase.nsf
 248   SRPDB                   Signal recognition particle database                            http://rnp.uthct.edu/rnp/SRPDB/SRPDB.html
 383   Subviral RNA DB         Database of viroids and viroid-like RNAs                        http://subviral.med.uottawa.ca/
 754   The Small Subunit       Modified nucleosides in small subunit rRNA                      http://library.med.utah.edu/SSUmods/
       rRNA Modification DB
 250   tmRDB                   tmRNA database                                                  http://rnp.uthct.edu/rnp/tmRDB/tmRDB.html
 249   tmRNA Website           tmRNA sequences and alignments                                  http://www.indiana.edu/~tmrna
 251   tRNA Sequences                                                                          Has not been updated
1148   Vir-Mir db              Prediction of viral microRNA candidate hairpins                 http://alk.ibms.sinica.edu.tw
 254   Yeast snoRNA            Yeast small nucleolar RNAs                                      http://www.bio.umass.edu/biochem/rna-
       Database                                                                                sequence/Yeast_snoRNA_Database/snoRNA_DataBa
                                                                                               se.html

       3. Protein Sequence Databases

       3.1. General sequence databases
163    EXProt                  Sequences of proteins with experimentally verified function     http://www.cmbi.kun.nl/EXProt/
 88    MIPS resources          Munich Information Center for Protein Sequences databases       http://mips.gsf.de/
542    NCBI Protein database   All protein sequences: translated from GenBank and imported     http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Prot
                               from other protein databases                                    ein
714    PA-GOSUB                Protein sequences from model organisms, GO assignment and       http://www.cs.ualberta.ca/~bioinfo/PA/
                              subcellular localization
194    PIR                    Protein Information Resource                                      http://pir.georgetown.edu
565    PRF                    Protein research foundation database of peptides                  http://www.prf.or.jp/en/index.shtml
790    TCDB                   Transporter protein classification database                       http://www.tcdb.org/
775    UniParc                UniProt archive, a repository of all protein sequences            http://www.uniprot.org/database/archive.shtml
318    UniProt                Universal Protein knowledgebase, combined information from        http://www.uniprot.org
                              Swiss-Prot, TrEMBL, and PIR
 197   UniProtKB\Swiss-Prot   Formerly SwissProt, part of the UniProt knowledgebase             http://www.expasy.org/sprot
 198   UniProtKB\TrEMBL       Now UniProt/TrEMBL, part of the UniProt knowledgebase             http://www.uniprot.org/database/knowledgebase.shtml
 776   UniRef                 Clustered sets of related sequences from UniProt                  http://www.uniprot.org/database/nref.shtml
1165   UniSave                UniProtKB Sequence/Annotation Version Archive                     http://www.ebi.ac.uk/uniprot/unisave/
       3.2. Protein properties
 221   AAindex                Physicochemical properties of amino acids                         http://www.genome.ad.jp/aaindex/
 979   BindingDB              Binding affinities of protein-ligand and other complexes          http://www.bindingdb.org/bind/index.jsp
 806   CyBase                 Proteins with cyclic backbones                                    http://research1t.imb.uq.edu.au/cybase
 885   dbPTM                  Information on post-translational modification of proteins        http://dbptm.mbc.nctu.edu.tw/
 914   iProLINK               Annotated literature sources for protein features and names       http://pir.georgetown.edu/iprolink
1093   MALISAM                Manual alignments for structurally analogous motifs in proteins   http://prodata.swmed.edu/malisam
1094   MegaMotifbase          Structural motifs in protein families and superfamilies           http://caps.ncbs.res.in/MegaMotifbase/index.html
 954   PIDD                   Protein inter-atomic distances database                           http://pidd.math.iastate.edu
 854   PINT                   Protein-protein interactions thermodynamic database               http://pintdb.dyndns.org/index.html
 856   PPD                    Experimentally-determined protein pKa values                      http://www.jenner.ac.uk/ppd/
1120   PPT-DB                 Protein Property Prediction and Testing Database                  http://redpoll.pharmacy.ualberta.ca/PPT_DB/public_ht
                                                                                                ml/PPT_main.html
280    ProTherm               Thermodynamic data for wild-type and mutant proteins              http://gibk26.bse.kyutech.ac.jp/jouhou/protherm/prothe
                                                                                                rm.html
1176   PRTAD                  Protein residue torsion angle database                            http://www.math.iastate.edu/prtad
 783   REFOLD                 Experimental data on protein refolding and purification           http://refold.med.monash.edu.au
       3.3. Protein localization and targeting
 444   DBSubLoc -             Database of protein Subcellular Localization                      http://www.bioinfo.tsinghua.edu.cn/dbsubloc.html
 930   eSLDB                  eukaryotic proteins Subcellular Localization Database             http://gpcr.biocomp.unibo.it/esldb
1021   InterFil               Human Intermediate Filament database                              http://www.interfil.org
 836   LOCATE                 Subcellular localization of mouse proteins                        http://locate.imb.uq.edu.au/
1022   MiCroKit               Midbody, Centrosome and Kinetochore proteins                      http://bioinformatics.lcd-ustc.org/microkit/
 226   MitoDrome              Nuclear-encoded mitochondrial proteins of Drosophila              http://www2.ba.itb.cnr.it/MitoDrome/
  85   MitoRes                Nuclear genes coding for mitochondrial proteins                   http://www2.ba.itb.cnr.it/MitoNuc/
 375   NESbase                Nuclear export signals database                                   http://www.cbs.dtu.dk/databases/NESbase
 376   NLSdb                  Nuclear localization signals                                      http://cubic.bioc.columbia.edu/db/NLSdb/
704    NMPdb                    Nuclear matrix associated proteins database                       http://www.rostlab.org/db/NMPdb/
706    NOPdb:                   Nucleolar proteome database                                       http://www.lamondlab.com/NOPdb/
369    NPD                      Nuclear Protein Database                                          http://npd.hgu.mrc.ac.uk
182    Nuclear Receptor         Nuclear receptor superfamily                                      http://nrr.georgetown.edu/NRR/nrrhome.htm
       Resource
183    NUREBASE                 Nuclear hormone receptors database                                http://www.ens-
                                                                                                  lyon.fr/LBMC/laudet/nurebase/nurebase.html
 789   NURSA                    Nuclear receptor signaling atlas                                  http://www.nursa.org
 734   PSORTdb                  Protein subcellular localization in bacteria                      http://db.psort.org/
 745   Secreted Protein DB      Secreted proteins from human, mouse and rat                       http://spd.cbi.pku.edu.cn
1014   SUBA                     Subcellular localisation of Arabidopsis proteins                  http://www.suba.bcs.uwa.edu.au/
 587   THGS                     Transmembrane Helices in Genome Sequences                         http://pranag.physics.iisc.ernet.in/thgs/
1140   TopDB                    Topology Data Bank of transmembrane proteins                      http://topdb.enzim.hu
 589   Transmembrane             Transmembrane proteins with experimentally-characterized         http://bioinfo.si.hirosaki-u.ac.jp/~TMPDB/
       Protein Database         transmembrane topologies
       3.4. Protein sequence motifs and active sites
374    ASC                      Active Sequence Collection                                        http://bioinformatica.isa.cnr.it/ASC/
203    Blocks                   Alignments of conserved regions in protein families               http://blocks.fhcrc.org
438    COMe                     Co-Ordination of Metals etc.                                      http://www.ebi.ac.uk/come/
771    CoPS                     Comprehensive peptide signature database                          http://cops.igib.res.in/copsv2/index.html
440    CSA                      Catalytic Site Atlas                                              http://www.ebi.ac.uk/thornton-srv/databases/CSA/
666    eBLOCKS                  Highly conserved protein sequence blocks                          http://fold.stanford.edu/eblocks/acsearch.html
452    eF-site                  Electrostatic surface of Functional site                          http://ef-site.protein.osaka-u.ac.jp/eF-site
206    eMOTIF                   Protein sequence motif determination and searches                 http://motif.stanford.edu/emotif
986    FireDB                   Functionally important residues in protein structures             http://firedb.bioinfo.cnio.es/
207    InterPro                 Integrated resource of protein families, domains and functional   http://www.ebi.ac.uk/interpro
                                sites
179    Metalloprotein Site DB   Metal-binding sites in metalloproteins                            http://metallo.scripps.edu/
209    O-GLYCBASE               O- and C-linked glycosylation sites in proteins                   http://www.cbs.dtu.dk/databases/OGLYCBASE/
717    PDBSite                  3D structure of protein functional sites                          http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?-
                                                                                                  page+LibInfo+-newId+-lib+PDBSite
 187   Phospho.ELM              S/T/Y protein phosphorylation sites (former PhosphoBase)          http://phospho.elm.eu.org/
1003   Phospho3D                3D structures of protein phosphorylation sites                    http://cbm.bio.uniroma2.it/p3d/
 212   PRINTS                   Hierarchical gene family fingerprints                             http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/
 193   PROMISE                  Prosthetic centers and metal ions in protein active sites         http://metallo.scripps.edu/PROMISE/
 899   ProRule                  Functional and structural information on PROSITE profiles         http://www.expasy.org/prosite/prorule.html
 215   PROSITE                  Biologically-significant protein patterns and profiles            http://www.expasy.org/prosite
 732   ProTeus                  Signature sequences at the protein N- and C-termini               http://www.proteus.cs.huji.ac.il
 868   SitesBase                Known ligand binding sites in the PDB                             http://www.modelling.leeds.ac.uk/sb/
       3.5. Protein domain databases; protein classification
622    ADDA                Database of protein domain classification                              http://ekhidna.biocenter.helsinki.fi/sqgraph/pairsdb
288    BAliBASE            Benchmark database for comparison of multiple sequence                 http://www-igbmc.u-
                           alignments                                                             strasbg.fr/BioInfo/BAliBASE2/index.html
978    Benchmark           Protein classification benchmark collection: training/test sets for    http://net.icgeb.org/benchmark/
                           machine learning
786    BIOZON              Database of gene and protein familiy classification                    http://biozon.org
204    CDD                 Conserved domain database, includes protein domains from Pfam,         http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
                           SMART, COG and KOG databases
 205   CluSTr              Clusters of UniProt Knowledgebase and IPI proteins                     http://www.ebi.ac.uk/clustr/
  7    COG                 Clusters of orthologous groups of proteins                             http://www.ncbi.nlm.nih.gov/COG
 448   DomIns              Database of Domain Insertions                                          http://www.domins.org/
1068   eggNOG              Evolutionary genealogy of genes: Non-supervised Orthologous            http://eggnog.embl.de
                           Groups
1069   EPGD                Eukaryotic Paralog Group Database                                      http://epgd.biosino.org:8080/EPGD/
 963   EVEREST             Automatically generated protein domain families                        http://www.everest.cs.huji.ac.il
 671   FunShift            Functional divergence between the subfamilies of a protein             http://FunShift.cgb.ki.se
                           domain family
470    FusionDB            Database of bacterial and archaeal gene fusion events                  http://www.igs.cnrs-mrs.fr/FusionDB/
200    Hits                Database of protein domains and motifs                                 http://hits.isb-sib.ch
266    HSSP                Homology-derived structures of proteins                                http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-
                                                                                                  page+LibInfo+-lib+HSSP
 510   InterDom            Putative protein domain interactions                                   http://interdom.i2r.a-star.edu.sg/
 208   iProClass           Integrated protein classification database                             http://pir.georgetown.edu/iproclass/
 844   MulPSSM             Multiple PSSMs of structural and sequence families                     http://hodgkin.mbu.iisc.ernet.in/~mulpssm
1109   PairsDB             Pairwise alignments of all sequences in UniProt                        http://pairsdb.csc.fi
 274   PALI                Phylogeny and alignment of homologous protein structures               http://pauling.mbu.iisc.ernet.in/~pali
 552   PANTHER             Protein sequence evolution mapped to functions and pathways            http://www.pantherdb.org
 210   Pfam                Protein families: Multiple sequence alignments and profile hidden      http://pfam.sanger.ac.uk/
                           Markov models of protein domains
 981   PhyloFacts          Phylogenomic analysis of protein families                              http://phylogenomics.berkeley.edu/phylofacts/
 561   PIRSF               Family/superfamily classification of whole proteins                    http://pir.georgetown.edu/pirsf/
 214   ProDom              Protein domain families                                                http://prodom.prabi.fr/
 216   ProtoMap            Hierarchical classification of Swiss-Prot proteins                     http://protomap.cornell.edu
 567   ProtoNet            Hierarchical clustering of Swiss-Prot proteins                         http://www.protonet.cs.huji.ac.il/
 217   SBASE               Protein domain sequences and tools                                     http://www.icgeb.org/sbase
 867   SIMAP               Similarity matrix of proteins: precomputed similarity data             http://mips.gsf.de/simap/
1010   SISYPHUS            Structural alignments for proteins with non-trivial relationships      http://sisyphus.mrc-cpe.cam.ac.uk
 218   SMART               Simple modular architecture research tool: signalling, extracellular   http://smart.embl-heidelberg.de
                              and chromatin-associated protein domains
219    SUPFAM                 Grouping of sequence families into superfamilies                  http://pauling.mbu.iisc.ernet.in/~supfam
199    TIGRFAMs               TIGR protein families adapted for functional annotation           http://www.tigr.org/TIGRFAMs


       3.6. Databases of individual protein families
157    ABCdb                  Archaeal and bacterial ABC transporter database                   http://www-abcdb.biotoul.fr
156    Aminoacyl-tRNA         Aminoacyl-tRNA synthetase database                                http://rose.man.poznan.pl/aars/index.html
       synthetases database
1045   Animal Toxin DB        Database of animal toxins                                         http://protchem.hunnu.edu.cn/toxin
 412   ARAMEMNON              Arabidopsis thaliana membrane proteins and transporters           http://aramemnon.botanik.uni-koeln.de
1166   BACTIBASE              Database of bacteriocin natural antimicrobial peptides            http://www.pfba-lab.org/bactibase
 158   BacTregulators         Transcriptional regulators of AraC and TetR families              No longer maintained
 976   BANMOKI                Database of bacterial nucleoside monophosphate kinases            http://www.ces.clemson.edu/compbio/databases/kinas
                                                                                                es
1057   ChromDB                Chromatin-associated proteins in a broad range of organisms       http://www.chromdb.org
 923   cpnDB                  Chaperonin database                                               http://cpndb.cbr.nrc.ca/
1154   CREMOFAC               Database of chromatin remodeling factors                          http://www.jncasr.ac.in/cremofac/
 364   CSDBase                Cold Shock Domain database                                        http://www.chemie.uni-marburg.de/~csdbase/
1168   CyMoBase               Cytoskeletal and motor proteins database                          http://www.motorprotein.de/cymobase
1065   DB-PABP                Experimentally characterized polyanion-binding proteins           http://ppa.bcf.ku.edu/DB_PABP/
 658   DCCP                   Database of Copper-Chelating Proteins                             http://sdbi.sdut.edu.cn/DCCP/en/index.php
 945   Defensins              Antimicrobial peptides of the defensin family                     http://defensins.bii.a-star.edu.sg/
       Knowledgebase
160    DExH/D Family DB       DEAD-box, DEAH-box and DExH-box proteins                          http://www.helicase.net/dexhd/dbhome.htm
892    DSD                    Database of dehydrogenase stereospecificities                     http://www.jenner.ac.uk/DSD
161    Endogenous GPCR List   G protein-coupled receptors; expression in cell lines             http://www.tumor-gene.org/GPCR/gpcr.html
814    EROP-Moscow            Database of Endogenous Regulatory OligoPeptides                   http://erop.inbi.ras.ru
162    ESTHER                 Esterases and other alpha/beta hydrolase enzymes                  http://bioweb.ensam.inra.fr/ESTHER/general?what=in
                                                                                                dex
 164   FUNPEP                 Low-complexity peptides capable of forming amyloid plaque         http://www.cmbi.kun.nl/swift/FUNPEP/gergo/
 166   GPCRDB                 G protein-coupled receptors database                              http://www.gpcr.org/7tm/
 679   gpDB                   G-protein database: G-proteins and their interaction with GPCRs   http://bioinformatics.biol.uoa.gr/gpDB
1085   Heme Protein DB        Heme protein structure, heme type, axial ligands, and heme        http://heme.chem.columbia.edu/heme.php
                              protein reduction potential (Em) values
167    Histone Database       Histone fold sequences and structures                             http://research.nhgri.nih.gov/histones/
365    HIV RT and Protease    HIV reverse transcriptase and protease sequences                  http://hivdb.stanford.edu
       Sequence Database
169    Homeobox Page          Homeobox proteins, classification, and evolution                  http://www.biosci.ki.se/groups/tbu/homeo.html
170    Homeodomain            Homeodomain sequences, structures, and related genetic and        http://research.nhgri.nih.gov/homeodomain/
       Resource                  genomic information
174    InBase                    Inteins (protein splicing elements) database: properties,         http://www.neb.com/neb/inteins.html
                                 sequences, bibliography
518    KinG                      Kinases in Genomes: Ser/Thr/Tyr kinases encoded in the            http://hodgkin.mbu.iisc.ernet.in/~king
                                 completely sequenced genomes
519    Knottin database          Database of knottins, small proteins with an unusual "disulfide   http://knottin.cbs.cnrs.fr/
                                 through disulfide" knot
176    LGICdb                    Ligand-gated ion channel subunit sequences database               http://www.pasteur.fr/recherche/banques/LGIC/LGIC.h
                                                                                                   tml
 368   Lipase Engineering DB     Sequence, structure and function of lipases and esterases         http://www.led.uni-stuttgart.de/
 524   LOX-DB                    Mammalian, invertebrate, plant and fungal lipoxygenases           http://www.dkfz-heidelberg.de/spec/lox-db/
 177   MEROPS                    Database of proteolytic enzymes (peptidases)                      http://merops.sanger.ac.uk/
1105   NORINE                    Database of nonribosomal peptides                                 http://bioinfo.lifl.fr/norine/
 546   NucleaRDB                 Nuclear receptor superfamily                                      http://www.receptors.org/NR/
 184   Olfactory Receptor DB     Sequences for olfactory receptor-like molecules                   http://senselab.med.yale.edu/senselab/ordb/
 186   Peptaibol                 Peptaibol (antibiotic peptide) sequences                          http://www.cryst.bbk.ac.uk/peptaibol/
 560   PhytoProt                 Clusters of (predicted) plant proteins                            http://urgi.versailles.inra.fr/phytoprot/
 189   PLANT-PIs                 Plant protease inhibitors                                         http://bighost.area.ba.cnr.it/PLANT-Pis
 371   PlantsP/PlantsT           Plant proteins involved in phosphorylation and transport          http://plantsp.sdsc.edu
 759   PLPMDB                    Pyridoxal-5'-phosphate dependent enzymes mutations                http://www.studiofmp.com/plpmdb/
 609   ProLysED                  Database of bacterial protease systems                            http://genome.ukm.my/prolyses/
 192   Prolysis                  Proteases and natural and synthetic protease inhibitors           http://delphi.phys.univ-tours.fr/Prolysis/
 188   Protein kinase resource   Protein kinase resource: sequences, enzymology, genetics and      http://www.kinasenet.org/pkr/
                                 molecular and structural properties
 224   REBASE                    Restriction enzymes and associated methylases                     http://rebase.neb.com/rebase/rebase.html
 195   RNAse P Database          Ribonuclease P sequences, alignments and structures               http://www.mbio.ncsu.edu/RNaseP/home.html
 901   RNRdb                     Ribonucleotide reductase database                                 http://rnrdb.molbio.su.se/
 573   RPG                       Ribosomal Protein Gene database                                   http://ribosome.miyazaki-med.ac.jp/
 575   RTKdb                     Receptor Tyrosine Kinase database                                 http://pbil.univ-lyon1.fr/RTKdb/
 372   SDAP                      Structural database of allergenic proteins and food allergens     http://fermi.utmb.edu/SDAP
1131   SelenoDB                  Database of selenoprotein genes, proteins and SECIS elements      http://www.selenodb.org/
 196   SENTRA                    Sensory signal transduction proteins                              http://compbio.mcs.anl.gov/sentra/
 373   SEVENS                    7-transmembrane helix receptors (G-protein-coupled)               http://sevens.cbrc.jp/1.20/
1137   Telomerase database       Sequences and structures of the RNA and protein subunits of       http://telomerase.asu.edu
                                 telomerase, mutations of telomerase components
311    TransportDB               Predicted membrane transporters in complete genomes, classified   http://www.membranetransport.org
                                 according to the TC classification system
                                                  +
399    VKCDB                     Voltage-gated K Channel Database                                  http://vkcdb.biology.ualberta.ca/
202    Wnt Database              Wnt proteins and phenotypes                                       http://www.stanford.edu/~rnusse/wntwindow.html
       4. Structure Databases

       4.1. Small molecules
 402   AANT                   Amino Acid - Nucleotide interaction database                       http://aant.icmb.utexas.edu/
 646   ChEBI                  Chemical entities of biological interest                           http://www.ebi.ac.uk/chebi/
1024   ChemBank               Structures and biological activities of small organic molecules    http://chembank.broad.harvard.edu/
1023   ChemDB                 3D structures and properties of small molecules                    http://cdb.ics.uci.edu
 261   CSD                    Cambridge Structural Database                                      http://www.ccdc.cam.ac.uk/prods/csd/csd.html
 360   Het-PDB Navi           Hetero-atoms in protein structures                                 http://daisy.bio.nagoya-u.ac.jp/golab/hetpdbnavi.html
 265   HIC-Up                 Hetero-compound Information Centre - Uppsala                       http://xray.bmc.uu.se/hicup/
 111   Klotho                 Collection and categorization of biological compounds              http://www.biocheminfo.org/klotho/
 113   LIGAND                 Chemical compounds and reactions in biological pathways            http://www.genome.ad.jp/ligand/
 615   PDB-Ligand             3D structures of small molecules bound to proteins and nucleic     http://www.idrtech.com/PDB-Ligand/
                              acids
 735   PubChem                Structures and biological activities of small organic molecules    http://pubchem.ncbi.nlm.nih.gov/
1127   R.E.DD.B.              RESP and ESP atomic charges and force field libraries for small    http://q4md-forcefieldtools.org/REDDB
                              molecules and molecular fragments
       4.2. Carbohydrates
 977   BCSDB/Glycoscience     Bacterial Carbohydrate Structure DataBase                          http://www.glyco.ac.ru/bcsdb/start.shtml
 429   CarbBank               CCSD - Complex Carbohydrate Structure Database                     http://bssv01.lancs.ac.uk/gig/pages/gag/carbbank.htm
 652   CSS                    Carbohydrate Structure Suite: carbohydrate 3D structures           http://www.dkfz.de/spec/css/
 486   Glycan                 Carbohydrate database, part of the KEGG system                     http://glycan.genome.ad.jp/
1080   Glycoconjugate Data    Annotated structures of glycan molecules                           http://daisy2.nagahama-i-bio.ac.jp/structures/
       Bank
988    GlycoMaps DB           Conformational maps of disaccharides                               http://www.glycosciences.de/modeling/glycomapsdb/
292    GlycoSuiteDB           N- and O-linked glycan structures and biological sources           http://www.glycosuite.com
535    Monosaccharide         Space filling Fischer projections of monosaccharides               http://www.terravivida.com/vivida/monosaccharide/
       Browser
300    SWEET-DB               Annotated carbohydrate structure and substance information         http://www.dkfz-heidelberg.de/spec2/sweetdb/
       4.3. Nucleic acid structure
1082   Greglist               G-quadruplex motifs and potentially G-quadruplex regulated genes   http://tubic.tju.edu.cn/greglist/
1090   ITS2                   Predicted structures of internal transcribed spacer 2 (ITS2)       http://its2.bioapps.biozentrum.uni-
                              molecules                                                          wuerzburg.de/ITS2_db.html
 272   NDB                    Nucleic acid-containing structures                                 http://ndbserver.rutgers.edu/
 273   NTDB                   Thermodynamic data for nucleic acids                               http://ntdb.chem.cuhk.edu.hk
1126   QuadBase               G-quadruplex motifs in the promoters of human, chimpanzee, rat,    http://quadbase.igib.res.in/
                              mouse and bacterial genes
1129   RNA FRABASE            Database of 3D RNA fragments within known RNA structures              http://rnafrabase.ibch.poznan.pl/
 387   RNABase                RNA-containing structures from PDB and NDB                            http://www.rnabase.org
1130   RNAJunction            RNA structural elements: helical junctions, internal loops, bulges    http://rnajunction.abcc.ncifcrf.gov
                              and loop-loop interactions
908    SARS-CoV RNA SSS       Predicted secondary structures of SARS coronavirus RNA                http://www.liuweibo.com/sarsdb/
283    SCOR                   Structural classification of RNA: RNA motifs by structure, function   http://scor.lbl.gov
                              and tertiary interactions
       4.4. Protein structure
401    3D-Genomics            Structural annotations for complete proteomes                         http://www.sbg.bio.ic.ac.uk/3dgenomics
633    3DID                   3D interacting domains                                                http://gatealoy.pcb.ub.es/3did/
413    ArchDB                 Automated classification of protein loop structures                   http://gurion.imim.es/archdb
255    ASTRAL                 Sequences of domains of known structure, selected subsets and         http://astral.berkeley.edu/
                              sequence-structure correspondences
1047   AutoPSI                Automated structural classification of protein sequences              http://www.bio.ifi.lmu.de/AutoPSIDB
 257   BioMagResBank          NMR spectroscopic data from proteins, peptides, and nucleic acids     http://www.bmrb.wisc.edu/
 384   CADB                   Conformational Angles DataBase of Proteins                            http://cluster.physics.iisc.ernet.in/cadb/
 258   CATH                   Protein domain structures database                                    http://www.cathdb.info/
 259   CE                     Combinatorial Extension method to compute and review 3D               http://cl.sdsc.edu/ce.html
                              protein structure alignments
 260   CKAAPs DB              Conserved Key Amino Acid Positions Database                           No longer maintained
 882   CoC Central            Universally conserved residues in protein folds                       http://kulibin.mit.edu/coc/
1059   ColiSNP                Mapping non-synonymous SNPs on protein structures                     http://yayoi.kansai.jaea.go.jp/colisnp
 883   Columba                Annotation of protein structures from the PDB                         http://www.columba-db.de
 442   Dali database          Fold classification based on structural alignment of proteins         http://ekhidna.biocenter.helsinki.fi/dali/start
1169   DBAli                  Database of structure alignments                                      http://salilab.org/DBAli/
 385   Decoys-R-Us            Computer-generated protein conformations based on sequence            http://dd.compbio.washington.edu/
                              data
447    DisProt                Database of Protein Disorder                                          http://divac.ist.temple.edu/disprot
809    DMAPS                  Database of multiple alignments for protein structures                http://bioinformatics.albany.edu/~dmaps
264    DSDBASE                Disulfide Database                                                    http://www.ncbs.res.in/~faculty/mini/dsdbase/dsdbase.
                                                                                                    html
386    DSMM                   A Database of Simulated Molecular Motions                             http://projects.villa-bosch.de/dbase/dsmm/
456    E-MSD                  EBI-Macromolecular Structure Database                                 http://www.ebi.ac.uk/msd
818    FSN                    Flexible structural neighborhood, structural neighbors of proteins    http://fatcat.ljcrf.edu/fatcat-
                              identified by FATCAT tool                                             cgi/cgi/struct_neibor/fatcatStructNeibor.pl
469    FSSP                                                                                         Superseded by the Dali database, no. 442
472    Gene3D                 Precalculated structural assignments for whole genomes                http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/
489    Genomic Threading DB   Structural annotations of complete genomes                            http://bioinf.cs.ucl.ac.uk/GTD
322   GTOP                      Protein fold predictions from genome sequences                       http://spock.genes.nig.ac.jp/~genome/gtop.html
498   HOMSTRAD                  Homologous structure alignment database: curated structure-          http://www-cryst.bioc.cam.ac.uk/homstrad
                                based alignments for protein families
267   IMB Jena Image Library    Visualization and analysis of 3D biopolymer structures               http://www.imb-jena.de/IMAGE.html
502   IMGT/3Dstructure-DB       3D structures of Immunoglobulins, T cell receptors, and MHC          http://imgt3d.igh.cnrs.fr/
                                proteins
829   IMOTdb                    Spatially interacting motifs in proteins                             http://caps.ncbs.res.in/imotdb/
269   LPFC                      Library of protein family core structures                            http://helix-web.stanford.edu/LPFC/
270   MMDB                      All experimentally-determined 3D structures, linked to NCBI Entrez   http://www.ncbi.nlm.nih.gov/Structure/
331   ModBase                   Annotated comparative protein structure models                       http://salilab.org/modbase
262   MolMovDB                  Database of Macromolecular Movements                                 http://bioinfo.mbb.yale.edu/MolMovDB/
107   MPID                      MHC-Peptide Interaction Database                                     http://surya.bic.nus.edu.sg/mpidt
275   PASS2                     Structural motifs of protein superfamilies                           http://www.ncbs.res.in/~faculty/mini/campass/pass2.ht
                                                                                                     ml
276   PDB                       Protein Data Bank: all known protein structures                      http://www.pdb.org/
619   PDB_TM                    Transmembrane proteins with known 3D structure                       http://pdbtm.enzim.hu/
277   PDB-REPRDB                Representative protein chains, based on PDB entries                  http://mbs.cbrc.jp/pdbreprdb-cgi/reprdb_menu.pl
278   PDBsum                    Summaries and analyses of PDB structures                             http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/
557   PepConfDB                 Database of peptide conformations                                    http://www.peptidome.org/products/list.htm
719   PFD                       Protein Folding Database : Experimental data on protein folding      http://www.foldeomics.org/pfd/public_html/index.php
855   PMDB                      3D protein models obtained from structure predictions                http://www.caspur.it/PMDB/
281   RESID                     Post-translational modifications of proteins                         http://www.ebi.ac.uk/RESID/
740   S4                        Structure-based Sequence Alignments of SCOP Superfamilies            http://compbio.mds.qmw.ac.uk/~james/S4.shtml
282   SCOP                      Structural classification of proteins                                http://scop.mrc-lmb.cam.ac.uk/scop
863   SCOPPI                    Structural classification of protein-protein interfaces              http://www.scoppi.org
284   SLoop                     Classification of protein loops                                      http://www-cryst.bioc.cam.ac.uk/~sloop/
530   SSToSS                    Sequence-Structural Templates of Single-member Superfamilies         http://caps.ncbs.res.in/SSTOSS/index.htm
785   STING Report              Amino acid properties in proteins of known structure                 http://sms.cbi.cnptia.embrapa.br/SMS/STINGm/SMSR
                                                                                                     eport/
583   Structure Superposition   Pairwise superpositions of 115 TIM-barrel structures                 http://ssd.rbvi.ucsf.edu/
      Database
285   SUPERFAMILY               Assignments of proteins to structural superfamilies                  http://supfam.org/SUPERFAMILY/
584   SURFACE                   Surface residues and functions annotated, compared and               http://cbm.bio.uniroma2.it/surface
                                evaluated: a database of protein surface patches
585   SWISS-MODEL               3D protein structure models generated by automated homology          http://swissmodel.expasy.org/repository
      Repository                modeling using SWISS-MODEL
764   TargetDB                  Target data from worldwide structural genomics projects              http://targetdb.pdb.org/
938   TMBETA-GENOME             Beta-barrel membrane proteins encoded in various genomes             http://tmbeta-genome.cbrc.jp/annotation/
941   TOPOFIT-DB                Protein structural alignments based on the TOPOFIT method            http://mozart.bio.neu.edu/topofit/
310   TOPS                      Topology Of Protein Structures                                       http://www.tops.leeds.ac.uk
       5. Genomics Databases (non-human)

       5.1. Genome annotation terms, ontologies and nomenclature
 915   BioThesaurus         A collection of gene/protein names and associated sequences         http://pir.georgetown.edu/iprolink/biothesaurus
1075   FunSimMat            Gene Ontology-based functional similarity values for proteins and   http://gotax.bioinf.mpi-inf.mpg.de/funsimmat/
                            protein families
487    GO                   Gene ontology consortium database                                   http://www.geneontology.org/
389    GOA                  Gene Ontology Annotation                                            http://www.ebi.ac.uk/GOA
939    GOPaD                Gene Ontology Partition Database                                    http://bcl.med.harvard.edu/proj/gopart
 73    HGNC Database        The HUGO Gene Nomenclature Database (formerly Genew)                http://www.genenames.org/
513    IUBMB Nomenclature   Nomenclature of enzymes, membrane transporters, electron            http://www.chem.qmul.ac.uk/iubmb/
       database             transport proteins and other proteins
514    IUPAC Nomenclature   Nomenclature of biochemical and organic compounds approved          http://www.chem.qmul.ac.uk/iupac/
       database             by the IUBMB-IUPAC Joint Commission
515    IUPHAR-RD            International Union of Pharmacology recommendations on              http://www.iuphar-db.org/iuphar-rd/
                            receptor nomenclature and drug classification
926    Plant Ontology DB    Controlled vocabulary of plant structures and growth stages         http://www.plantontology.org
358    SOURCE               Functional genomics resource for human, mouse and rat               http://source.stanford.edu
906    TreeBase             Phylogenetic trees and the data matrices used to generate them      http://www.treebase.org/
317    UMLS                 Unified medical language system                                     Requires user registration
       5.2. Taxonomy and identification
1018   GeneTrees            Pre-compiled alignments and gene phylogenies for a variety of       http://genetrees.vbi.vt.edu
                            taxonomic groups
  78   ICB                  gyrB database for identification of bacteria                        http://seasquirt.mbio.co.jp/icb/
1088   IDBD                 Infectious Disease Biomarker Database                               http://biomarker.korea.ac.kr
 297   NCBI Taxonomy        Names of all organisms that are represented in GenBank              http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhom
       Browser                                                                                  e.html
 299   RIDOM                Ribosomal Differentiation of Medical Microorganisms                 http://www.ridom.de/
1135   SuperCAT             Database for multilocus sequence typing analysis of the Bacillus    http://mlstoslo.uio.no/
                            cereus group of bacteria
301    Tree of Life         Information on phylogeny and biodiversity                           http://phylogeny.arizona.edu/tree/phylogeny.html
965    VNTR Locus DB        Bacterial Variable Number Tandem Repeat locus database              http://vntr.csie.ntu.edu.tw/
       5.3. General genomics databases
641    BacMap               Picture atlas of annotated bacterial genomes                        http://wishart.biology.ualberta.ca/BacMap/
650    CoGenT++             Complete genome tracking: Predicted peptides from fully             http://cgg.ebi.ac.uk/cgg/cpp_sitemap.html
                            sequenced genomes
 445   DEG                  Database of Essential Genes                                       http://tubic.tju.edu.cn/deg
1172   diArk                Database of eukaryotic sequencing projects                        http://www.diark.org/diark/
 451   EBI Genomes          EBI’s collection of databases for the analysis of complete and    http://www.ebi.ac.uk/genomes
                            unfinished viral, pro- and eukaryotic genomes
458    Entrez Genomes       NCBI’s collection of databases for the analysis of complete and   http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Ge
                            unfinished viral, pro- and eukaryotic genomes                     nome
461    ERGO-Light           Integrated biochemical data on 10 bacterial genomes: Publicly-    http://www.ergo-light.com/
                            available portion of the ERGO database
 674   GenDiS               Genomic distribution of protein structural superfamilies          http://caps.ncbs.res.in/gendis/home.html
 327   GeneNest             Gene indices of human, mouse, zebrafish, etc.                     http://genenest.molgen.mpg.de/
1077   GenoList             An integrated environment for comparative analysis of microbial   http://genolist.pasteur.fr/
                            genomes
484    Genome Information   DDBJ’s collection of genome databases                             http://gib.genes.nig.ac.jp
       Broker
678    Genome Reviews       Integrated view of complete genomes                               http://www.ebi.ac.uk/GenomeReviews/
916    Genome Project DB    NCBI's database of large-scale genome sequencing projects         http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=s
                                                                                              earch&DB=genomeprj
75     GOLD                 Genomes online database: a listing of completed and ongoing       http://www.genomesonline.org/
                            genome projects
830    HOINVGEN             Homologous invertebrate genes                                     http://pbil.univ-
                                                                                              lyon1.fr/databases/hoinvgen/HOINVGEN.html
690    Inparanoid           Database of eukaryotic orthologs                                  http://inparanoid.cgb.ki.se/
223    Integr8              Functional classification of proteins in whole genomes            http://www.ebi.ac.uk/integr8/
777    KaryotypeDB          Karyotype and chromosome data for animal and plant species        http://www.nenno.it/karyotypedb/
112    KEGG                 Kyoto Encyclopedia of Genes and Genomes: databases on genes,      http://www.genome.ad.jp/kegg
                            proteins, and metabolic pathways
 528   MBGD                 Microbial genome database for comparative analysis                http://mbgd.genome.ad.jp/
 114   MetaCyc              Metabolic pathways and enzymes from various organisms             http://metacyc.org/
1103   Narcisse             Conserved syntenies for various animal, plant and bacterial       http://narcisse.toulouse.inra.fr
                            genomes
 703   NegProt              Negative Proteome: A tool for comparison of complete proteomes    http://superfly.ucsd.edu/negprot
1040   NMPDR                Database for functional annotation and comparative analysis of    http://www.nmpdr.org
                            microbial genomes
1106   OPTIC                Orthologous and Paralogous Transcripts in Clades                  http://genserv.anat.ox.ac.uk/
 549   ORFanage             Orphan ORFs (ORFs with no homologs) in microbial genomes          No longer maintained
1108   OrthoDB              An hierarchical catalog of orthologous proteins in metazoa        http://cegg.unige.ch/orthodb/browse
 847   OrthoMCL             Orthologous protein clusters from multiple genomes                http://orthomcl.cbil.upenn.edu
 715   PartiGeneDB          Assembled partial genomes for ~250 eukaryotic organisms           http://www.partigenedb.org/
 354   PEDANT               Results of an automated analysis of genomic sequences             http://pedant.gsf.de
 377   PEP                  Predictions for Entire Proteomes                                  http://cubic.bioc.columbia.edu/pep/
1113   PhylomeDB                Experimentally validated and predicted serine phosphorylation sites   http://phylomedb.bioinfo.cipf.es
                                in Arabidopsis thaliana
118    PUMA2                    Metabolic analysis of complete microbial genomes                      http://compbio.mcs.anl.gov/puma2/
582    STRING                   Predicted functional associations between proteins                    http://string.embl.de/
 66    TIGR Comprehensive       Various data on complete microbial genomes: Uniform annotation,       http://www.tigr.org/tigr-
       Microbial Resource       properties of DNA and predicted proteins                              scripts/CMR2/CMRHomePage.spl
  5    TIGR Gene Indices        Organism-specific databases of EST and gene sequences                 http://www.tigr.org/tdb/tgi.shtml
 99    TIGR Microbial DB        A list of microbial genome sequencing projects                        No longer maintained
877    VBI Microbial Database   Virginia Bioinformatics Institute microbial database                  http://phytophthora.vbi.vt.edu
       5.4. Viral genome databases
1051   BioHealthBase            Host-pathogen interactions of influenza virus                         http://dev.biohealthbase.org/GSearch/PrototypeIndex
                                                                                                      .jsp
1061   CoVDB                    Database of coronavirus genes and genomes                             http://covdb.microbiology.hku.hk
 810   DPVweb                   Descriptions of plant viruses                                         http://www.dpvweb.net
1034   euHCVdb                  European Hepatitis C Virus database                                   http://euhcvdb.ibcp.fr
 492   HCV Database             Hepatitis C Virus (HCV) Sequence Database                             http://hcv.lanl.gov/
 473   HCVdb                    Hepatitis C Virus Database                                            http://hepatitis.ibcp.fr/
 972   HepSeq                   Epidemiological, clinical, and sequence data on the Hepatitis B       http://www.hpa-bioinfodatabases.org.uk/
                                virus                                                                 hepatitis_open/main.php
495    HERVd                    Human Endogenous Retrovirus database                                  http://herv.img.cas.cz
497    HIV Drug Resistance      HIV mutations that confer resistance to anti-HIV drugs                http://resdb.lanl.gov/Resist_DB/default.htm
       Database
168    HIV Molecular            HIV epitopes                                                          http://hiv-web.lanl.gov/immunology/
       Immunology Database
990    HIV Positive Selection   Positively selected mutations in HIV-1 protease and reverse           http://bioinfo.mbi.ucla.edu/HIV
       Mutation Database        transcriptase
909    Influenza Virus          Protein and nucleotide sequences of the influenza virus               http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html
       Resource
993    IVDB                     Influenza Virus Database : Annotated sequences and geographic         http://influenza.genomics.org.cn
                                distribution of the influenza virus
602    NCBI Viral Genomes       Viral genome resource at NCBI                                         http://www.ncbi.nlm.nih.gov/genomes/VIRUSES/virus
                                                                                                      es.html
725    Poxvirus.org             Poxvirus genomic sequences and gene annotation                        http://www.poxvirus.org
750    T4-like genome DB        Sequences of T4-like bacteriophages from various sources              http://phage.bioc.tulane.edu
201    VIDA                     Homologous viral protein families database                            http://www.biochem.ucl.ac.uk/bsm/virus_database/VI
                                                                                                      DA.html
761    VIPERdb                  Virus particle explorer: Virus capsid structures                      http://viperdb.scripps.edu/
798    Viral Bioinformatics     Virus orthologous genes, gene families and genomes                    http://www.biovirus.org
       Resource Center
 397   VirGen                    Curated database for complete viral genome sequences               http://bioinfo.ernet.in/virgen/virgen.html
1039   ViTa                      microRNAs targets of the influenza virus                           http://vita.mbc.nctu.edu.tw
       5.5. Prokaryotic genome databases
       5.5.1. General
1044   AlterORF                  Database of alternate open reading frames                          http://www.cienciavida.cl/alterorf/
 641   BacMap                    Picture atlas of annotated bacterial genomes                       http://wishart.biology.ualberta.ca/BacMap
 884   Comparative               DNA walks, nucleotide skews and other biometric measures of        http://www.unil.ch/comparativegenometrics/
       Genometrics               prokaryotic genomes
70     EMGlib                    Enhanced microbial genomes library: Completely sequenced           http://pbil.univ-lyon1.fr/emglib/emglib.html
                                 genomes of unicellular organisms
 328   GeneDB                    Curated database for various Sanger-sequenced genomes              http://www.genedb.org/
 611   Genome Atlas              DNA structural properties of sequenced genomes                     http://www.cbs.dtu.dk/services/GenomeAtlas/
1084   HEG-DB                    Predicted highly expressed genes in prokaryotic genomes            http://genomes.urv.cat/HEG-DB
 352   HGT-DB                    Horizontal Gene Transfer-DataBase                                  http://www.fut.es/~debb/HGT/
 828   IMG                       Comparative analysis of microbial genomes sequenced at the DOE     http://img.jgi.doe.gov/
                                 Joint Genome Institute
1089   IMG/M                     A data management and analysis system for metagenomes              http://img.jgi.doe.gov/m
 826   Interrupted coding        Interrupted coding sequences: frameshifts, stop codons,            http://www-bio3d-igbmc.u-strasbg.fr/ICDS/
       sequences DB              sequencing errors in microbial genomes
837    MeGX                      Marine ecological genomix: genomics and metagenomics of marine     http://www.Megx.net
                                 bacteria
 614   MetaGrowth                Growth requirements of bacterial pathogens                         http://igs-server.cnrs-mrs.fr/axenic/
 959   MiST                      Microbial Signal Transduction database                             http://genomics.ornl.gov/mist/
 720   PGTdb                     Prokaryotic growth temperature database                            http://pgtdb.csie.ncu.edu.tw/
  43   RRNDB                     rRNA operon numbers in various prokaryotes                         http://rrndb.cme.msu.edu
1160   Roundup                   Repository of orthologs and corresponding evolutionary distances   http://rodeo.med.harvard.edu/tools/roundup
 866   SIDDBase                  Stress-induced DNA duplex destabilization profiles of complete     http://www.genomecenter.ucdavis.edu/benham/siddb
                                 microbial genomes                                                  ase/
426    xBase                     A family of group-specific bacterial genome databases, includes    http://xbase.bham.ac.uk/
                                 coliBASE, CampyDB, ClostriDB, MycoDB, PseudoDB and others
       5.5.2. Escherichia coli
415    ASAP                      A Systematic Annotation Package                                    https://asap.ahabs.wisc.edu/annotation/php/ASAP1.h
                                                                                                    tm
428    CCDB                      CyberCell Database                                                 http://redpoll.pharmacy.ualberta.ca/CCDB
436    coliBase                  Database for E. coli, Salmonella and Shigella                      http://colibase.bham.ac.uk/
437    Colibri                                                                                      http://genolist.pasteur.fr/Colibri/
623    EchoBASE                  Post-genomic studies of Escherichia coli                           http://www.ecoli-york.org/
108    EcoCyc                    E. coli K12 genes, pathways, transporters, and gene regulation     http://ecocyc.org/
  69   EcoGene                    Sequence and literature data on E. coli genes and proteins            http://ecogene.org/
1070   ERIC                       Enteropathogen Resource Integration Center                            http://www.ericbrc.org
 462   Essential genes in E.      A list of genes essential for viability of E. coli                    http://www.genome.wisc.edu/resources/essential.htm
       coli
482    GenoBase                   Functional genomic aAnalysis of E. coli in Japan                      http://ecoli.aist-nara.ac.jp/
165    GenProtEC                  E. coli K12 genome and proteome database                              http://genprotec.mbl.edu
       5.5.3. Bacillus subtilis
424    BSORF                      Bacillus subtilis Open Reading Frames                                 http://bacillus.genome.ad.jp/
 31    DBTBS                      Bacillus subtilis promoters and transcription factors                 http://dbtbs.hgc.jp/
 89    NRSub                      Non-redundant Bacillus subtilis database at U. Lyon                   http://pbil.univ-lyon1.fr/nrsub/nrsub.html
 96    SubtiList                  Bacillus subtilis genome database at Institut Pasteur                 http://genolist.pasteur.fr/SubtiList/
       5.5.4. Other bacteria
1153   BuchneraBase               Genomic database for the pea aphid symbiont Buchnera sp. APS          http://www.buchnera.org/
 426   CampyDB                    Campylobacter Database                                                Incoroporated into xBase, no. 426
 648   CIDB                       Chlamydia Interactive Database: Gene expression data                  http://www.it.deakin.edu.au/CIDB
 433   ClostriDB                  Clostridium Database                                                  Incoroporated into xBase, no. 426
1167   CoryneRegNet               Corynebacterial transcription factors                                 http://www.coryneregnet.de
  68   CyanoBase                  Cyanobacterial genomes                                                http://www.kazusa.or.jp/cyano/
 834   LEGER                      Post-genome research of Listeria                                      http://leger2.gbf.de/cgi-bin/expLeger.pl
 521   LeptoList                  Leptospira interrogans genome                                         http://www.bioinfo.hku.hk/LeptoList/.
 534   MolliGen                   Genomic data on mollicutes                                            http://cbi.labri.fr/outils/molligen/
 896   MtbRegList                 Mycobacterium tuberculosis gene regulation                            http://www.USherbrooke.ca/vers/MtbRegList
 996   MvirDB                     Protein toxins, virulence factors, and antibiotic resistance genes    http://mvirdb.llnl.gov/
 944   PAIDB                      Pathogenicity islands in bacterial genomes                            http://www.gem.re.kr/paidb
1000   PATRIC                     PathoSystems Resource Integration Center                              https://patric.vbi.vt.edu
 555   PEC                        Profiling of E. coli Chromosome                                       http://shigen.lab.nig.ac.jp/ecoli/pec
 720   PGTdb                      Prokaryotic growth temperature database                               http://pgtdb.csie.ncu.edu.tw/
 733   PseudoCAP                  Pseudomonas aeruginosa community genome annotation project            http://www.pseudomonas.com/
 947   RegTransBase               Manually curated database of regulatory interactions in prokaryotes   http://regtransbase.lbl.gov
  94   RsGDB                      Rhodobacter sphaeroides genome                                        http://www.hgsc.bcm.tmc.edu/projects/microbial/Rsph
                                                                                                        aeroides/
 865   ShiBase                    Shigella database                                                     http://www.mgc.ac.cn/ShiBASE/
 760   VFDB                       Virulence Factors of pathogenic bacteria                              http://www.mgc.ac.cn/cgi-bin/VFs/compatho.cgi
1017   xanthusBase                Genome of the social bacterium Myxococcus xanthus                     http://www.xanthusbase.org/
       5.5.5. Archaea
964    Sulfolobus Database        Comparative genomics of Sulfolobus species                            http://www.sulfolobus.org
876    UCSC Archaeal              Pyrococcus furiosus genome browser                                    http://archaea.ucsc.edu/
       Genome Browser
       5.6. Unicellular eukaryotes genome databases
 969   ApiDB                   Unified resource for various apicomplexan species                  http://ApiDB.org
 409   ApiDots                 EST sequences from various Apicomplexan parasites                  http://www.cbil.upenn.edu/apidots/
 983   Comparasite             Database for comparative study of parasite cDNAs                   http://comparasite.hgc.jp/
 439   CryptoDB                Cryptosporidium database                                           http://cryptodb.org/
 662   Diatom EST DB           ESTs from diatom algae Thalassiosira and Phaeodactylum             http://www.biologie.ens.fr/diatomics/EST/
 446   DictyBase               Universal resource for Dictyostelium discoideum                    http://dictybase.org/
  72   Full-Malaria            Full-length cDNA library from erythrocytic-stage Plasmodium        http://fullmal.ims.u-tokyo.ac.jp
 917   ParameciumDB            Paramecium genome sequencing project                               http://paramecium.cgm.cnrs-gif.fr/db/index
  91   PlasmoDB                Plasmodium genome database                                         http://PlasmoDB.org
1124   ProtozoaDB              Comparative analysis of protozoan genomes                          http://protozoa.biowebdb.org/
 912   TBestDB                 Taxonomically broad EST database: protist ESTs                     http://tbestdb.bcm.umontreal.ca/
 586   TcruziDB                Trypanosoma cruzi genome database                                  http://tcruzidb.org/
 359   ToxoDB                  Toxoplasma gondii genome database                                  http://ToxoDB.org
 910   U-genome                Genome organization in unicellular eukaryotes                      http://sege.ntu.edu.sg/wester/ugenome/
       5.7. Fungi
1056   CFGP                    Comparative Fungal Genomics Platform                               http://cfgp.snu.ac.kr
 955   Fungal Genome Size      Genome sizes of various fungi                                      http://www.zbi.ee/fungal-genomesize/
       Database
       5.7.1. Yeasts
635    AGD                     Ashbya gossypii genome database                                    http://agd.unibas.ch
617    CandidaDB               Candida albicans genome database                                   http://genolist.pasteur.fr/CandidaDB
645    Candida Genome          Candida albicans genome database                                   http://www.candidagenome.org/
441    CYGD                    MIPS Comprehensive yeast genome database                           http://mips.gsf.de/proj/yeast
483    Génolevures             A comparison of S. cerevisiae and 14 other yeast species           http://cbi.labri.fr/Genolevures
841    Mpact                   Yeast protein-protein interaction data                             http://mips.gsf.de/genre/proj/mpact
730    PROPHECY                Profiling of phenotypic characteristics in yeast                   http://prophecy.lundberg.gu.se/
576    SCMD                    Saccharomyces cerevisiae morphological database: micrographs of    http://yeast.gi.k.u-tokyo.ac.jp/
                               budding yeast mutants
577    SCPD                    Saccharomyces cerevisiae promoter database                         http://rulai.cshl.edu/SCPD/
357    SGD                     Saccharomyces genome database                                      http://www.yeastgenome.org/
 25    TRIPLES                 Transposon-insertion phenotypes, localization, and expression in   http://ygac.med.yale.edu/triples/
                               Saccharomyces
306    YDPM                    Yeast deletion project and mitochondria database                   http://www-
                                                                                                  deletion.stanford.edu/YDPM/YDPM_index.html
342    Yeast Intron Database   Ares lab database of splicesomal introns in S. cerevisiae          http://www.cse.ucsc.edu/research/compbio/yeast_
                                                                                                  introns.html
792   YEASTRACT               Yeast search for transcriptional regulators and consensus tracking   http://www.yeastract.com
254   Yeast snoRNA DB         Yeast small nucleolar RNAs                                           http://www.bio.umass.edu/biochem/rna-sequence/
                                                                                                   Yeast_snoRNA_Database/snoRNA_DataBase.html
791   YGOB                    Yeast gene order browser                                             http://wolfe.gen.tcd.ie/ygob
307   yMGV                    Yeast microarray global viewer                                       http://www.transcriptome.ens.fr/ymgv/
531   YMPD                    Yeast mitochondrial protein database                                 http://bmerc-www.bu.edu/projects/mito/
763   YRC PDR                 Yeast resource center public data repository                         http://www.yeastrc.org/pdr/
      5.7.2. Other fungi
425   CADRE                   Central Aspergillus data repository                                  http://www.cadre.man.ac.uk/
435   COGEME                  Phytopathogenic fungi and oomycete EST database                      http://cogeme.ex.ac.uk
815   FGDB                    MIPS Fusarium graminearum genome database                            http://mips.gsf.de/genre/proj/fusarium/
525   Magnaporthe grisea DB   Magnaporthe grisea Database                                          http://www.broad.mit.edu/annotation/genome/magnap
                                                                                                   orthe_grisea/Home.html
533   MNCDB                   MIPS Neurospora crassa database                                      http://mips.gsf.de/proj/neurospora/
708   OGD                     Oomycete Genomics Database: ESTs and annotation                      http://www.oomycete.net/
852   PHI-base                Genes affecting fungal pathogen-host interactions                    http://www4.rothamsted.bbsrc.ac.uk/phibase/
 98   Phytophthora Functio-   ESTs and expression data from P. infestans and P. sojae              http://www.pfgd.org/pfgd/
      nal Genomics DB
      5.8. Invertebrates
      5.8.1. Caenorhabditis elegans
430   C. elegans Project      Genome sequencing data at the Sanger Institute                       http://www.sanger.ac.uk/Projects/C_elegans
238   Intronerator            Introns and splicing in C. elegans and C. briggsae                   http://www.cse.ucsc.edu/~kent/intronerator/
570   RNAiDB                  RNAi phenotypic analysis of C. elegans genes                         http://www.rnai.org/
864   SGCEdb                  Structural genomics of C. elegans                                    No longer maintained
304   WorfDB                  C. elegans ORFeome                                                   http://worfdb.dfci.harvard.edu/
 51   WormBase                Data repository for C. elegans and C. briggsae: curated genome       http://www.wormbase.org/
                              annotation, genetic and physical maps, pathways
961   WormBook                Peer-reviewed chapters on the biology of C. elegans                  http://www.wormbook.org
      5.8.2. Drosophila melanogaster
774   DPDB                    Drosophila polymorphism database                                     http://dpdb.uab.es/
928   DroID                   Drosophila gene and protein interaction data                         http://www.droidb.org/
449   Drosophila microarray   Canadian Drosophila microarray centre                                http://www.flyarrays.com/
      centre
924   DroSpeGe                Drosophila Species Genomes                                           http://insects.eugenes.org/DroSpeGe/
816   FLIGHT                  Drosophila phenotypes, gene expression and protein interactions      http://flight.licr.org/
 71   FlyBase                 Drosophila sequences and genomic information                         http://flybase.org/
767   FlyBrain                Database of the Drosophila nervous system                            http://flybrain.neurobio.arizona.edu/
 670   FlyMine                Integration of insect genomic and proteomic data                  http://www.flymine.org
 817   FlyRNAi DRSC           Genome-wide RNAi analysis data in Drosophila                      http://flyRNAi.org/cgi-bin/RNAi_screens.pl
1073   FLYSNP                 Single nucleotide polymorphism data for Drosophila melanogaster   http://flysnp.imp.univie.ac.at
1158   FlyTF                  Drosophila Transcription Factors                                  http://www.mrc-lmb.cam.ac.uk/genomes/FlyTF/
 467   FlyTrap                Drosophila mutants created using protein trap strategy            http://flytrap.med.yale.edu/
  14   FlyView                Drosophila development and genetics                               http://flyview.uni-muenster.de/
 471   GadFly                 Genome annotation database of Drosophila                          http://www.fruitfly.org
 677   GeniSys                Enhancer- and promoter-inserted mutants of Drosophila             http://genisys.kaist.ac.kr:8080
 989   GenomeRNAi             Cell-based RNAi phenotypes database                               http://www.dkfz.de/signaling/ernai/ernai.html
   8   Homophila              Drosophila homologs of human disease genes                        http://superfly.ucsd.edu/homophila/
 509   InterActive Fly        Drosophila genes and their roles in development                   http://www.sdbonline.org/fly/aimain/1aahome.htm
1128   REDfly                 Regulatory modules and transcription factor binding sites in      http://redfly.ccr.buffalo.edu
                              Drosophila
       5.8.3. Other invertebrates
  63   ACeDB                  C. elegans, S. pombe, and human genomic information               http://www.acedb.org/
1152   AphidBase              Genomic database for the pea aphid (Acyrthosiphon pisum)          http://www.aphidbase.com/
 410   AppaDB                 Database on the nematode Pristionchus pacificus                   http://appadb.eb.tuebingen.mpg.de
 643   BeetleBase             Genome database of the beetle Tribolium castaneum                 http://www.bioinformatics.ksu.edu/BeetleBase/
1052   ButterflyBase          Genomics of butterflies (Lepidoptera)                             http://www.butterflybase.org
 649   Ciliate IES-MDS Db     Macro- and micronuclear genes in spirotrichous ciliates           http://oxytricha.princeton.edu/dimorphism/database.ht
                                                                                                m
 434   CnidBase               Cnidarian evolution and gene expression database                  http://cnidbase.bu.edu/
 653   CuticleDB              Structural proteins of Arthropod cuticle                          http://bioinformatics.biol.uoa.gr/cuticleDB.
 698   LumbriBASE             ESTs of the earthworm Lumbricus rubellus                          http://www.earthworms.org
 543   Nematode.net           Parasitic nematode sequencing project                             http://nematode.net/
 544   NEMBASE                Nematode sequence and functional data database                    http://www.nematodes.org
 726   PPNEMA                 Plant-parasitic nematode rRNAs                                    http://www.ppnema.uniba.it/
1006   Pristionchus.org       Genome data of the nematode <I>Pristionchus pacificus</I>         http://www.pristionchus.org
1161   Sebida                 Sex bias in insect gene expression database                       http://www.sebida.de
 743   SilkDB                 Silkworm Bombyx mori ESTs, mutants, photographs                   http://www.ab.a.u-tokyo.ac.jp/genome/
 744   SilkSatDb              A microsatellite database of the silkworm Bombyx mori             http://210.212.212.7:9999/PHP/SILKSAT/index.php
1133   SmedGD                 The Schmidtea mediterranea genome database                        http://smedgd.neuro.utah.edu
 747   SpodoBase              Genomics of the butterfly Spodoptera frugiperda                   http://bioweb.ensam.inra.fr/spodobase/
 871   StellaBase             Nematostella vectensis (sea anemone) genome                       http://stellabase.org.
 873   Tetrahymena Genome     Tetrahymena thermophila genome database                           http://www.ciliate.org
       DB
1031   VectorBase             Invertebrate Vectors of Human Pathogens                           http://www.vectorbase.org
 925   wFleaBase              Daphnia Water Flea Genome Database                                http://wfleabase.org/
       6. Metabolic Enzymes and Pathways; Signaling Pathways
898    Pathguide               A listing of pathway, signal transduction and protein-protein      http://pathguide.org
                               interaction databases
       6.1. Enzymes and enzyme nomenclature
421    BRENDA                  Enzyme names and biochemical properties                            http://www.brenda-enzymes.info/
109    ENZYME                  Enzyme nomenclature and properties                                 http://www.expasy.org/enzyme/
459    Enzyme Nomenclature     IUBMB Nomenclature Committee recommendations                       http://www.chem.qmul.ac.uk/iubmb/enzyme/
613    EzCatDB                 Enzyme Catalytic Mechanism Database                                http://mbs.cbrc.jp/EzCatDB/
716    FCP                     Functional coverage of the proteome by structures                  http://cgl.imim.es/fcp/
508    IntEnz                  Integrated enzyme database and enzyme nomenclature                 http://www.ebi.ac.uk/intenz
893    MACiE                   Mechanism, annotation and classification in enzymes: enzyme        http://www.ebi.ac.uk/thornton-srv/databases/MACiE/
                               reaction mechanisms
 998   ORENZA                  ORphan ENZymes database                                            http://www.orenza.u-psud.fr/
 727   PRECISE                 Predicted and Consensus Interaction Sites in Enzymes               http://precise.bu.edu/precisedb/
1121   PROCOGNATE              Protein cognate ligands for the domains in enzyme structures       http://www.ebi.ac.uk/thornton-
                                                                                                  srv/databases/procognate/index.html
758    SCOPEC                  Mapping of catalytic function to domain structure                  http://www.sbinf.org/~richard/enzome/
772    TECRdb                  Thermodynamics of enzyme-catalyzed reactions                       http://xpdb.nist.gov/enzyme_thermodynamics
       6.2. Metabolic pathways
419    BioCarta                Online maps of metabolic and signaling pathways                    http://www.biocarta.com/genes/allPathways.asp
420    BioCyc                  Pathway/genome databases for many bacteria                         http://biocyc.org/
423    Biodegradative Strain   Microorganisms that can degrade aromatic and other organic         http://bsd.cme.msu.edu/
       Database                compounds
644    BioSilico               Integrated access to various metabolic databases                   http://biosilico.kaist.ac.kr
991    HMDB                    The Human Metabolome Database: Curated human metabolite and        http://www.hmdb.ca
                               metabolism data
112    KEGG Pathway            Metabolic and regulatory pathways in complete genomes              http://www.genome.jp/kegg/pathway.html
835    Lipid MAPS              Lipid metabolites and pathways strategy                            http://www.lipidmaps.org
114    MetaCyc                 Metabolic pathways and enzymes from various organisms              http://metacyc.org
115    PathDB                  Biochemical pathways, compounds and metabolism                     No longer maintained
612    Reactome                Database of metabolic and signaling pathways                       http://www.reactome.org/
953    SYSTOMONAS              SYSTems biology of pseudOMONAS                                     http://www.systomonas.de/
117    UM-BBD                  University of Minnesota biocatalysis and biodegradation database   http://umbbd.msi.umn.edu/
       6.3. Protein-protein Interactions
633    3DID                     3D interacting domains: Domain-domain interactions in proteins    http://3did.embl.de/
                                 with known 3D structures
1042   3D-Interologs             Protein-protein interactions in various evolutionary lineages           http://gemdock.life.nctu.edu.tw/3D-Interologs
 796   AffinDB                   Affinity data for protein-ligand complexes                              http://www.agklebe.de/affinity
 405   aMAZE                     A system for the annotation, management, and analysis of                http://www.scmbb.ulb.ac.be/amaze/
                                 biochemical and signalling pathway networks
1046   AtPID                     Arabidopsis thaliana Protein Interactome Database                       http://atpid.biosino.org/
1048   Bacteriome.org            Protein interaction database for E. coli                                http://www.bacteriome.org
 103   BIND                      Biomolecular interaction network database                               No longer free for all
1049   Binding MOAD              Binding Mother of All Databases: protein-ligand crystal structures      http://www.BindingMOAD.org
 800   BioGRID                   Genetic and physical interactions in yeast, worm and fly                http://www.thebiogrid.org
 422   BRITE                     Biomolecular Relations in Information Transmission and                  http://www.genome.ad.jp/brite
                                 Expression
980    CellCircuits              Molecular network models: from pairwise molecular interactions to       http://www.cellcircuits.org
                                 whole pathways
1060   CORUM                     Experimentally verified mammalian protein complexes                     http://mips.gsf.de/genre/proj/corum
 946   CutDB                     Community annotation resource for proteases, their substrates           http://cutdb.burnham.org/
                                 and cleavage sites
 659   DDIB                      Database of domain interactions and binding                             http://www.ddib.org/
1066   DIMA                      Domain interaction map: experimental data and predictions on            http://mips.gsf.de/genre/proj/dima2
                                 protein domain interactions
104    DIP                       Database of interacting proteins: Experimentally-determined             http://dip.doe-mbi.ucla.edu
                                 protein-protein interactions
1155   Dockground                Protein-protein interfaces in co-crystallized protein structures        http://dockground.bioinformatics.ku.edu/
1067   DOMINE                    Known and predicted protein domain interactions in PDB entries          http://domine.utdallas.edu
1033   DOMINO                    Domain peptide interactions                                             http://mint.bio.uniroma2.it/domino/
 105   DRC                       Database of ribosomal crosslinks                                        http://www.mpimg-berlin-
                                                                                                         dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc/
1086   HotSprint                 Hot spots (functionally and structurally important residues) in         http://prism.ccbb.ku.edu.tr/hotsprint/
                                 protein interfaces
664    hp-DPI                    Database of protein interactions in Helicobacter pylori                 http://dpi.nhri.org.tw/hp/
688    HPID                      Human protein interaction database                                      http://www.hpid.org
897    I2D                       Interologous Interaction Database: Predicted protein-protein            http://ophid.utoronto.ca/i2d
                                 interactions in humans
 507   IntAct                    Protein-protein interaction data                                        http://www.ebi.ac.uk/intact/
 770   Inter-Chain Beta-Sheets   Protein interactions mediated by interchain beta-sheet formation        http://www.igb.uci.edu/servers/icbs/
 510   InterDom                  Putative protein domain interactions                                    http://interdom.i2r.a-star.edu.sg/
 138   KDBI                      Kinetic data of bio-molecular interactions                              http://bioinf.xmu.edu.cn/databases/kdbi/kdbi.php
1091   LigAsite                  Biologically relevant binding sites in proteins with known structures   http://www.scmbb.ulb.ac.be/Users/benoit/LigASite
 942   MiMI                      Michigan Molecular Interactions: Protein-protein interactions           http://mimi.ncibi.org/MiMI/home.jsp
1032   MINT                      Molecular INTeraction                                                   http://mint.bio.uniroma2.it/mint/
 897   OPHID                    Online predicted human interaction database                         Superseded by I2D (no. 897)
 718   PDZBase                  Protein-protein interactions involving PDZ domains                  http://icb.med.cornell.edu/services/pdz/start
1111   PepCyber:P~Pep           Human protein interactions mediated by phosphoprotein-binding       http://PepCyber.umn.edu/PepCyber
                                domains
773    PINdb                    Proteins interacting in nucleus (human and yeast)                   http://pin.mskcc.org
748    POINT                    Prediction of human protein-protein interactome                     http://point.bioinformatics.tw
729    ProNIT                   Protein-nucleic acid interactions                                   http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.ht
                                                                                                    ml
 943   PROTCOM                  3D structures of two-chain protein complexes                        http://www.ces.clemson.edu/compbio/protcom
 616   PSIbase                  Interaction of proteins with known 3D structures                    http://psimap.org/index.php/PSIMAP
1012   SNAPPI                   Structures, iNterfaces and Alignments for Protein-Protein           http://www.compbio.dundee.ac.uk/SNAPPI/download
                                Interactions                                                        s.jsp
1134   STITCH                   Search Tool for Interactions of Chemicals                           http://stitch.embl.de
 749   Structurally conserved   Interacting residues in protein-protein interfaces in PDB           http://home.ku.edu.tr/~okeskin/INTERFACE/INTERF
       interfaces                                                                                   ACES.html
1138   The Cell Cycle DB        Genes and proteins involved in human and yeast cell cycle           http://www.itb.cnr.it/cellcycle
 960   UniHI                    Unified Human Interactome: human protein-protein interactions       http://www.mdc-berlin.de/unihi
       6.4. Signaling pathways
 419   BioCarta                 Online maps of metabolic and signaling pathways                     http://www.biocarta.com/genes/allPathways.asp
 794   Cyclonet                 Database on cell cycle regulation                                   http://cyclonet.biouml.org/index.html
 890   EndoNet                  Information on endocrine networks                                   http://endonet.bioinf.med.uni-goettingen.de/
1038   Hedgehog signalling      Resources and annotations of the Hedgehog signaling pathway         http://hedgehog.sfsu.edu/
1104   NetworKIN                Network approach to human protein kinases and their substrates      http://networkin.info/
1112   PhosPhAt                 Arabidopsis Protein Phosphorylation Site Database                   http://www.plantenergy.uwa.edu.au/applications/phos
                                                                                                    phat/index.html
1175   PRRDB                    Pattern recognition receptors and their ligands                     http://www.imtech.res.in/raghava/prrdb/
 858   pSTIING                  Protein signalling, transcriptional interactions and inflammation   http://pstiing.licr.org/
                                networks gateway
 571   ROSPath                  Reactive oxygen species (ROS) signaling pathway                     http://rospath.ewha.ac.kr
 395   STCDB                    Signal Transduction Classification Database                         http://bibiserv.techfak.uni-bielefeld.de/stcdb/
1142   UCSD-Nature Signaling    Expert-authored and peer-reviewed information on mammalian          http://www.signaling-gateway.org/molecule/
       Gateway                  proteins involved in cellular signaling
       7. Human and other Vertebrate Genomes
       7.1. Model organisms, comparative genomics
879    ABA                     Ascidian body atlas: digital 3D model of ascidian development    http://ciona.lab.nig.ac.jp/ascidian/top.html
974    AgBase                  GO annotations for agriculturally important plants and animals   http://www.agbase.msstate.edu/
 26    AllGenes                Human and mouse gene, transcript and protein annotation          http://www.allgenes.org
957    Animal Genome Size      Genome sizes of vertebrates and invertebrates                    http://www.genomesize.com
       Database
 975   AnimalQTLdb             Quantitative trait loci in livestock animals                     http://www.animalgenome.org/QTLdb/
  65   ArkDB                   Genome databases for farm and other animals                      http://www.thearkdb.org/
  12   BodyMap                 Human and mouse gene expression data                             http://bodymap.ims.u-tokyo.ac.jp/
 881   BodyMap-Xs              Cross-species comparison of vertebrate gene expression           http://bodymap.jp/
 647   ChickVD                 Sequence variation in the chicken genome                         http://chicken.genomics.org.cn
 286   Cre Transgenic DB       Cre transgenic mouse lines with links to publications            http://www.mshri.on.ca/nagy/
 337   CORG                    COmparative Regulatory Genomics: conserved non-coding blocks     http://corg.molgen.mpg.de
 808   DBTGR                   Database of tunicate Ciona gene regulation                       http://dbtgr.hgc.jp/
 660   DED                     Database of evolutionary distances                               No longer maintained
  20   Edinburgh Mouse Atlas   Digital atlas of mouse embryonic development                     http://genex.hgu.mrc.ac.uk
 453   EGO                     Eukaryotic Gene Orthologs                                        http://compbio.dfci.harvard.edu/tgi/ego/
  27   Ensembl                 Annotated information on eukaryotic genomes                      http://www.ensembl.org/
 396   euGenes                 Genomic Information for Eukaryotic Organisms                     http://eugenes.org/
1071   EuroPhenome             Large-scale phenotyping of knockout mouse lines                  http://www.europhenome.eu
 673   GALA                    Genomic alignment, annotation and experimental results           http://gala.cse.psu.edu/
1076   Gallus Gbrowse          Genomic information on chicken and other avian species           http://birdbase.net/
1173   GEISHA                  Gallus expression in situ hybridization analysis                 http://geisha.arizona.edu
  15   GXD                     Mouse Gene Expression Database                                   http://www.informatics.jax.org/menus/expression_me
                                                                                                nu.shtml
605    HomoloGene              Automatically detected homologous genes in complete eukaryotic   http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=ho
                               genomes                                                          mologene
  8    Homophila               Drosophila homologs of human disease genes                       http://superfly.ucsd.edu/homophila/
400    KOG                     Eukaryotic Orthologous Groups of proteins                        http://www.ncbi.nlm.nih.gov/COG/
952    MamPol                  Mammalia Polymorphism Database                                   http://mampol.uab.es
839    MFunGD                  MIPS mouse functional genomics database                          http://mips.gsf.de/genre/proj/mfungd
 87    Mouse Genome DB         Formerly mouse genome database                                   http://www.informatics.jax.org
995    Mouse Phenome DB        phenotypic and genotypic data from inbred strains of mice        http://www.jax.org/phenome
537    Mouse SAGE              SAGE libraries from various mouse tissues and cell lines         http://mouse.biomed.cas.cz/sage
540    Mouse Transposon        Mouse Transposon Insertion Database                              http://mouse.ccgb.umn.edu/transposon/
       Insertion Database
152    Mouse Tumor Biology     Tumor types, genes, classification, incidence, pathology            http://tumor.informatics.jax.org
598    Non-Human Genome        Segmental duplications in mouse, dog and chicken genomes            http://projects.tcag.ca/xenodup
       Segmental Duplication
       DB
 548   OMIA                    Online Mendelian Inheritance in Animals                             http://omia.angis.org.au/
 553   ParaDB                  Paralogy mapping in human genomes                                   http://abi.marseille.inserm.fr/paradb/
 554   PathBase                European mutant mice histopathology database: images                http://www.pathbase.net/
1110   PBmice                  piggyBac transposon insertions in the mouse genome.                 http://www.scbit.org/PBmice/
 556   PEDE                    Pig Expression Data Explorer: Pig cDNA libraries and ESTs           http://pede.dna.affrc.go.jp
 936   PigGIS                  Pig genome mapping, genes and ESTs                                  http://pig.genomics.org.cn/
  93   Rat Genome Database     Rat genetic and genomic data                                        http://rgd.mcw.edu
 625   RatMap                  Rat genome tools and data                                           http://ratmap.org
 574   RTCGD                   Retroviral Tagged Cancer Gene Database                              http://rtcgd.ncifcrf.gov/
1164   SPEED                   Searchable prototype experimental evolutionary database             http://bioinfobase.umkc.edu/speed/speed_main.htm
 751   TAED                    The Adaptive Evolution Database: plant and chordate gene families   http://www.bioinfo.no/tools/TAED
 875   TreeFam                 Tree families database: phylogenetic trees of animal genes          http://www.treefam.org
1144   UniTrap                 Unambiguous insertions in the same subgenic regions of annotated    http://unitrap.cbm.fvg.it/
                               mouse genes
1145   UTGB/medaka             University of Tokyo Genome Browser of medaka fish (Oryzias          http://medaka.utgenome.org/
                               latipes) genomic data
784    VEGA                    Vertebrate genome annotation: a repository for manual annotation    http://vega.sanger.ac.uk/
                               of finished vertebrate genome sequences
1150   XenBase                 Xenopus genomics resource                                           http://www.xenbase.org
 101   ZFIN                    Zebrafish information network                                       http://zfin.org/
       7.2. Human genome databases, maps and viewers
985    ENCODE Project          Encyclopedia of DNA Elements, all functional elements in the        http://genome.ucsc.edu/ENCODE
                               human genome
 56    GDB                     Human genes and genomic maps                                        http://www.gdb.org
 35    Gene Resource Locator   Alignment of ESTs with finished human sequence                      No longer maintained
326    GeneAnnot               Revised annotation of Affymetrix human gene probe sets              http://genecards.weizmann.ac.il/geneannot/
350    GeneCards               Integrated database of human genes, maps, proteins and diseases     http://bioinfo.weizmann.ac.il/genecards/
348    GeneLoc                 Gene location database                                              http://genecards.weizmann.ac.il/geneloc/
 59    GenMapDB                Mapped human BAC clones                                             http://genomics.med.upenn.edu/genmapdb
324    HOWDY                   Human organized whole genome database                               http://www-alis.tokyo.jst.go.jp/HOWDY/
 77    Human BAC Ends DB       Non-redundant human BAC end sequences                               http://www.tigr.org/tdb/humgen/bac_end_search/bac_
                                                                                                   end_intro.html
597    Human Genome Seg-       Segmental duplications in the human genome                          http://projects.tcag.ca/humandup
       mental Duplication DB
61     IXDB                    Physical maps of human chromosome X                                 http://ixdb.mpimg-berlin-dahlem.mpg.de
 54    Map Viewer            Display of genomic information by chromosomal position            http://www.ncbi.nlm.nih.gov/mapview/
859    QTL Matchmaker        Quantitative trait loci mapping in human, mouse and rat           http://pmrc.med.mssm.edu:9090/QTL/jsp/qtlhome.jsp
 62    RHdb                  Radiation hybrid map data                                         http://www.ebi.ac.uk/RHdb
592    SKY/M-FISH and CGH    Fluorescent images of chromosomes and cytogenetic data            http://www.ncbi.nlm.nih.gov/sky/
596    The Chromosome 7      Human chromosome 7 sequence and annotation                        http://www.chr7.org
       Annotation Project
684    TRBase                Tandem repeats in the human genome                                http://trbase.ex.ac.uk/
316    UCSC Genome           Genome assemblies and annotation                                  http://genome.ucsc.edu/
       Browser
319    UniSTS                Unified view of sequence tagged sites with mapping data           http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=uni
                                                                                               sts
1149   X:MAP                 Annotation and visualization of genome structure for Affymetrix   http://xmap.picr.man.ac.uk
                             exon array analysis
       7.3. Human proteins
 911   Consensus CDS         Collaborative effort to identify a core set of human proteins     http://www.ncbi.nlm.nih.gov/projects/CCDS/
1072   Evola                 Human genes and their vertebrate orthologs                        http://jbirc.jbic.or.jp/hinv/evola/
 465   FANTOM                Functional annotation of mouse full-length cDNA clones            http://fantom2.gsc.riken.go.jp
  37   FLJ-DB                Annotated full-length human cDNAs (formerly HUNT database)        http://fldb.hgc.jp/cgi-
                                                                                               bin/cDNA3/public/publication/index.cgi
1037   GeneSpeed             Protein domains in the expressed human, mouse, fly and worm       http://genespeed.ccf.org
                             genes
685    H-InvDB               Full-length human cDNA clones                                     http://www.h-invitational.jp/
687    Hoppsigen             Human and mouse homologous processed pseudogenes                  http://pbil.univ-lyon1.fr/databases/hoppsigen.html
500    HPRD                  Human protein reference database: domain architecture, post-      http://www.hprd.org
                             translational modifications, and disease association
171    HUGE                  Human unidentified gene-encoded large (>50 kDa) protein and       http://www.kazusa.or.jp/huge/
                             cDNA sequences
696    IPI                   International Protein Index                                       http://www.ebi.ac.uk/IPI
522    LIFEdb                Localization, interaction and functions of human proteins         http://www.dkfz.de/LIFEdb
600    Mammalian Gene        Full-length open reading frame clones for human, mouse, and rat   http://mgc.nci.nih.gov/
       Collection            genes
 545   NetAffx               Public Affymetrix probesets and annotations                       http://www.affymetrix.com/
 550   ORFDB                 Collection of ORFs that are sold by Invitrogen                    http://orf.invitrogen.com/
1028   PlasmID               A repository for collection and distribution of plasmid clones    http://plasmid.hms.harvard.edu/
  4    STACK                 Sequence tag alignment and consensus knowledgebase                http://www.sanbi.ac.za/Dbases.html
 220   SYSTERS               Systematic re-searching and clustering of proteins                http://systers.molgen.mpg.de/
 312   trome, trEST, trGEN   Databases of predicted human protein sequences                    ftp://ftp.isrec.isb-sib.ch/pub/databases/
  6    UniGene               Unified clusters of ESTs and full-length mRNA sequences           http://www.ncbi.nlm.nih.gov/UniGene/
       8. Human Genes and Diseases

       8.1. General human genetics databases
661    DG-CST                Disease gene conserved sequence tags                                  http://143.225.208.11/cst3/
 57    GenAtlas              Human genes, markers and phenotypes                                   http://www.genatlas.org/
479    Genetics Home         A general guide on human hereditary diseases                          http://ghr.nlm.nih.gov/
       Reference
680    HAGR                  Human ageing genomic resources: Genes related to ageing in            http://genomics.senescence.info/
                             humans and model organisms
683    HCAD                  Human chromosome aberration database: Chromosomal                     http://www.pdg.cnb.uam.es/UniPub/HCAD/
                             breakpoints and affected genes
 133   HGMD                  Human gene mutation database                                          Requires user registration
1087   Human PAML Browser    Positive selection in human genes detected through genome             http://mendel.gene.cwru.edu/adamslab/pbrowser.py
                             comparison
1100   MSY Breakpoint        Sequence-tagged sites in the human Y chromosome                       http://breakpointmapper.wi.mit.edu
       Mapper
1102   MutDB                 Predicted biochemical effects of human genetic variation: maping of   http://mutdb.org/
                             SNPs on protein sequence and structure
143    OMIM                  Online Mendelian inheritance in man: A catalog of human genetic       http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OM
                             and genomic disorders                                                 IM
1163   SNP2NMD               Human SNPs causing nonsense-mediated mRNA decay                       http://variome.kobic.re.kr/SNP2NMD/
       8.2. General polymorphism databases
119    ALFRED                Allele frequencies and DNA polymorphisms                              http://alfred.med.yale.edu
793    CTGA                  Database for genetic disorders in Arabs                               http://www.cags.org.ae
654    Cypriot national      Disease mutations in the Cypriot population                           http://www.goldenhelix.org/cypriot/
       mutation database
125    Cytokine Gene Poly-   Cytokine gene polymorphism literature database                        http://www.nanea.dk/cytokinesnps/
       morphism Database
655    Database of Genomic   Human genomic variants: frequency, segmental duplications and         http://projects.tcag.ca/variation/
       Variants              genome assembly gaps
595    dbQSNP                Quantification of SNP allele frequencies database                     http://qsnp.gen.kyushu-u.ac.jp/
886    dbRIP                 Human retrotransposon insertion polymorphism                          http://falcon.roswellpark.org:9090/
127    dbSNP                 Database of single nucleotide polymorphisms                           http://www.ncbi.nlm.nih.gov/SNP/
966    D-HaploDB             Definitive haplotype database                                         http://orca.gen.kyushu-u.ac.jp
669    FESD                  Functional Element SNPs Database: SNPs located within                 http://sysbio.kribb.re.kr/FESD/
                             promoters, UTRs, etc., of human genes
1020   FINDBase              Frequencies of INherited Disorders                                    http://www.findbase.org
1074   F-SNP                   Functional effects of various human SNPs                             http://compbio.cs.queensu.ca/F-SNP/
 344   HapMap Project          A haplotype map of the human genome with patterns of DNA             http://snp.cshl.org
                               sequence variation
131    HGVbase                 Human genome variation database: Curated human                       http://hgvbase.cgb.ki.se
                               polymorphisms
496    HGVS Databases          A compilation of human mutation databases                            http://www.hgvs.org/
517    JSNP                    Japanese SNP database                                                http://snp.ims.u-tokyo.ac.jp/
665    PhenomicDB              Comparison of phenotypes of orthologous genes in human and           http://www.phenomicdb.de
                               model organisms
 973   PolyDoms                Human coding SNPs mapped onto protein domains                        http://polydoms.cchmc.org
 724   Polymorphix             Database of sequence polymorphisms                                   http://pbil.univ-lyon1.fr/polymorphix/query.php
 146   Protein Mutant DB       Compilation of protein mutant data                                   http://pmd.ddbj.nig.ac.jp/
1011   SNAP                    An integrated SNP Annotation Platform                                http://platform.humgen.au.dk/
1030   SNP@Ethnos              Human SNPs and genes that contain human ethnic variation             http://bioportal.kobic.re.kr/SNPatETHNIC/
 626   SNPeffect & PupaSuite   Phenotypic effects of human coding SNPs                              http://snpeffect.vib.be/
 590   TopoSNP                 Topographic database of non-synonymous SNPs                          http://gila.bioengr.uic.edu/snp/toposnp
 755   TPMD                    Taiwan polymorphic microsatellite marker database                    http://tpmd.nhri.org.tw
       8.3. Cancer gene databases
122    Atlas of Genetics and   Cancer related genes, chromosomal abnormalities in oncology and      http://atlasgeneticsoncology.org/
       Cytogenetics in Onco-   haematology, and cancer-prone diseases
       logy and Haematology
593    Cancer Chromosomes      Cytogenetic, clinical, and reference information on cancer-related   http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=ca
                               aberrations                                                          ncerchromosomes
 951   CancerGenes             Gene selection resource for cancer genome projects                   http://cbio.mskcc.org/cancergenes
1053   CanGEM                  Gene copy number changes in cancer                                   http://www.cangem.org/
 431   CGED                    Cancer Gene Expression Database                                      http://lifesciencedb.jp/cged/
 651   COSMIC                  Catalogue Of Somatic Mutations In Cancer: Sequence data,             http://www.sanger.ac.uk/perl/CGP/cosmic
                               samples and publications
126    Database of Germline    Mutations in human tumor and cell line p53 gene                      http://www.lf2.cuni.cz/projects/germline_mut_p53.ht
       p53 Mutations                                                                                m
889    EHCO                    Encyclopedia of hepatocellular carcinoma genes online                http://ehco.iis.sinica.edu.tw
822    HPTAA                   Human potential tumor-associated antigens                            http://www.bioinfo.org.cn/hptaa/
134    Human p53, human        Mutations at the human p53 and hprt genes; rodent transgenic lacI    http://www.ibiblio.org/dnam/mainpage.html
       hprt, rodent lacI and   and lacZ mutations
       rodent lacZ databases
 362   IARC TP53 Database      Human TP53 somatic and germline mutations                            http://www-p53.iarc.fr/index.html
 833   ITTACA                  Integrated tumor transcriptome array and clinical data analysis      http://bioinfo.curie.fr/ittaca
1096   MethyCancer             Links between DNA methylation levels and cancer                      http://methycancer.genomics.org.cn
1026   OncoDB.HCC              Oncogenomic database of hepatocellular carcinoma                     http://oncodb.hcc.ibms.sinica.edu.tw
 153   Oral Cancer Gene DB    Cellular and molecular data for genes involved in oral cancer     Incorporated into TGDBs, no. 155
1125   PubMeth                Links between DNA methylation levels and cancer                   http://matrix.ugent.be/pubmeth/
 579   SNP500Cancer           Re-sequenced SNPs from 102 reference samples                      http://snp500cancer.nci.nih.gov
 149   SV40 Large T-Antigen   Mutations in SV40 large tumor antigen gene                        http://supernova.bio.pitt.edu/pipaslab/
       Mutant Database
922    Tumor Associated       Tumor-associated genes database                                   http://www.binfo.ncku.edu.tw/TAG/GeneDoc.php
       Gene Database
155    Tumor Gene Family      Cellular, molecular and biological data about genes involved in   http://www.tumor-gene.org/tgdf.html
       Databases (TGDBs)      various cancers
768    ALPSbase               Autoimmune lymphoproliferative syndrome database                  http://research.nhgri.nih.gov/ALPS/
       8.4. Gene-, system- or disease-specific databases
788    AlzGene                Candidate genes for Alzheimer disease                             http://www.alzgene.org
120    Androgen Receptor      Mutations in the androgen receptor gene                           http://www.mcgill.ca/androgendb/
       Gene Mutations DB
393    AngioDB                Database of angiogenesis and angiogenesis-related molecules       http://angiodb.snu.ac.kr/
416    BayGenomics            Publicly available mouse gene trap cell lines                     Superseded by Gene Trap database, no. 827
417    BGED                   Brain Gene Expression Database                                    http://genome.mc.pref.osaka.jp/BGED/
123    BTKbase                Mutation registry for X-linked agammaglobulinemia                 http://bioinf.uta.fi/BTKbase/
594    CarpeDB                Comprehensive database on the genetics of epilepsy                http://www.carpedb.ua.edu
124    CASRDB                 Calcium-sensing receptor database: CASR mutations causing         http://www.casrdb.mcgill.ca/
                              hypercalcemia and/or hyperparathyroidism
137    Collagen Mutation DB   Human type I and type III collagen gene mutations                 http://www.le.ac.uk/genetics/collagen/
887    DENIZ                  Beta-thalassemia allele frequencies in world populations          No longer maintained
454    EICO DB                Expression-based Imprint Candidate Organiser                      http://fantom2.gsc.riken.jp/EICODB/
110    EpoDB                  Genes expressed during human Erythropoiesis database              http://www.cbil.upenn.edu/EpoDB/
460    ERGDB                  Estrogen Responsive Genes Database                                http://sdmc.lit.org.sg/ergdb/cgi-bin/explore.pl
464    EyeSite                Families of proteins functioning in the eye                       http://eyesite.cryst.bbk.ac.uk/
363    GOLD.db                Genomics Of Lipid-associated Disorders                            http://gold.tugraz.at
130    HaemB                  Factor IX gene mutations, insertions and deletions                http://www.kcl.ac.uk/ip/petergreen/haemBdatabase.
                                                                                                html
491    HbVar                  Human hemoglobin variants and thalassemias                        http://globin.cse.psu.edu/globin/hbvar
907    HDBase                 A website for Huntington's disease research                       http://hdbase.org/
493    HemBase                Genes expressed in differentiating human erythroid cells          http://hembase.niddk.nih.gov/
494    HemoPDB                Hematopoietic Promoter Database                                   http://bioinformatics.med.ohio-state.edu/HemoPDB
366    HORDE                  Human Olfactory Receptor Data Exploratorium                       http://bioinfo.weizmann.ac.il/HORDE/
293    HOX-PRO                Homeobox genes database                                           http://www.iephb.nw.ru/labs/lab38/spirov/hox_pro/ho
                                                                                                x-pro00.html
499    HPMR                   Human plasma membrane receptome: sequences, literature, and       http://receptome.stanford.edu/
                              expression data
135    Human PAX2 Allelic       Mutations in human PAX2 gene                                        http://pax2.hgu.mrc.ac.uk/
       Variant Database
136    Human PAX6 Allelic       Mutations in human PAX6 gene                                        http://pax6.hgu.mrc.ac.uk/
       Variant Database
501    IL2Rgbase                X-linked severe combined immunodeficiency mutation database         http://research.nhgri.nih.gov/scid/
294    Imprinted Gene           Imprinted genes and parent-of-origin effects in animals             http://igc.otago.ac.nz/home.html
       Catalogue
506    INFEVERS                 Hereditary inflammatory disorder and familial mediterranean fever   http://fmf.igh.cnrs.fr/infevers
                                mutation data
949    KBERG                    KnowledgeBase for Estrogen Responsive Genes                         http://research.i2r.a-star.edu.sg/kberg
139    KinMutBase               Disease-causing protein kinase mutations                            http://www.uta.fi/imt/bioinfo/KinMutBase/
523    Lowe Syndrome            Mutations causing Lowe oculocerebrorenal syndrome                   http://research.nhgri.nih.gov/lowe/
       Mutation Database
 142   NCL Resource             Polymorphisms in neuronal ceroid lipofuscinoses genes               http://www.ucl.ac.uk/ncl/
1025   NEIbank                  EyeSAGE, EyeBrowse and Eye Disease Gene databases                   http://neibank.nei.nih.gov
 144   PAHdb                    Mutations at the phenylalanine hydroxylase locus                    http://www.pahdb.mcgill.ca
 559   PGDB                     Prostate and prostatic diseases gene database                       http://www.ucsf.edu/pgdb/
 145   PHEXdb                   PHEX mutations causing X-linked hypophosphatemia                    http://www.phexdb.mcgill.ca
 154   Prostate Expression DB   Prostate expression database: ESTs from prostate tissue and cell    http://www.pedb.org/
                                type-specific cDNA libraries
147    PTCH1 Mutation DB        Mutations and SNPs found in PTCH1 gene                              http://www.cybergene.se/cgi-bin/w3-
                                                                                                    msql/ptchbase/index.html
148    RB1 Gene Mutation DB     Mutations in the human retinoblastoma (RB1) gene                    http://www.verandi.de/joomla/
769    SCAdb                    Spinocerebellar ataxia candidate gene database                      http://ymbc.ym.edu.tw/sca_ensembl/
787    SynDB                    Synapse protein database                                            http://syndb.cbi.pku.edu.cn
632    T1Dbase                  A resource for type 1 diabetes research                             http://t1dbase.org
752    The Autism Chromoso-     Curated collection of genomic features related to autism            http://projects.tcag.ca/autism
       me Rearrangement DB
753    The Lafora Database      The Lafora progressive myoclonus epilepsy mutation and              http://projects.tcag.ca/lafora/
                                polymorphism database
907    T-REGs                   A list of TGFbeta-responsive genes                                  No longer maintained

       9. Microarray Data and other Gene Expression Databases
1043   4DXpress                 Database for cross species expression pattern comparisons           http://ani.embl.de/4DXpress
 634   5'SAGE                   5'-end serial analysis of gene expression                           http://5sage.gi.k.u-tokyo.ac.jp/
 338   ArrayExpress             Public collection of microarray gene expression data                http://www.ebi.ac.uk/arrayexpress
  11   Axeldb                   Gene expression in Xenopus laevis                                   http://www.dkfz.de/en/mol_embryology/axeldb.html
 802   CAGE                     CAGE tags for cap-analysis of gene expression                       http://fantom31p.gsc.riken.jp/cage/mm5/
 427   CATMA                    Complete Arabidopsis Transcriptome MicroArray                       http://www.catma.org
 432   CleanEx                  Expression reference database, linking heterogeneous expression     http://www.cleanex.isb-sib.ch/
                                 data to facilitate cross-dataset comparisons
1064   CycleBase                 Gene expression profiles from cell-cycle microarray studies         http://www.cyclebase.org
 657   dbERGEII                  Database of experimental results on gene expression: Genomic        http://dberge.cse.psu.edu/menu.html
                                 alignment, annotation and experimental data
1170   dbLEP                     Database of Liver proteome expression profiles                      http://lep.hupo.org.cn/main.htm
 812   EMAGE                     Edinburgh mouse atlas gene expression database                      http://genex.hgu.mrc.ac.uk/Emage/database
  13   EPConDB                   Gene expression in pancreatic development, beta cell function and   http://www.cbil.upenn.edu/EPConDB
                                 diabetes
987    Gene Aging Nexus          Aging-related gene expression data                                  http://gan.usc.edu
 24    Gene Expression in        Gene expression in dental tissue                                    http://bite-it.helsinki.fi/
       Tooth Database
325    GeneNote                  Human genes expression profiles in healthy tissues                  http://genecards.weizmann.ac.il/genenote/
330    GenePaint                 Gene expression patterns in the mouse                               http://www.genepaint.org/Frameset.html
676    GeneTide                  A transcriptome-focused member of the GeneCards suite               http://genecards.weizmann.ac.il/genetide/
481    GeneTrap                  Expression patterns in an embryonic stem library of gene trap       http://www.cmhd.ca/genetrap/
                                 insertions
918    GENSAT                    Gene Expression Nervous System Atlas: a map of gene expression      http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=ge
                                 in the central nervous system of the mouse                          nsat
603    GEO                       Gene Expression Omnibus: Public gene expression repository          http://www.ncbi.nlm.nih.gov/geo/
485    GermOnline                Gene expression in mitotic and meiotic cell cycle                   http://www.germonline.org/
891    GPX-Macrophage            Gene expression in macrophages                                      http://ebola.gti.ed.ac.uk:8090/GPX/htdocs/index.html
 23    HuGEIndex                 Human Gene Expression Index: Expression levels in normal            http://zlab.bu.edu/HugeSearch
                                 tissues
16     Interferon Stimulated     Genes induced by treatment with interferons                         http://www.lerner.ccf.org/labs/williams/xchip-html.cgi
       Gene Database
827    International Gene Trap   Publicly available gene trap cell lines in mouse                    http://www.genetrap.org/
       Consortium DB
17     Kidney Development        Kidney development and gene expression                              http://golgi.ana.ed.ac.uk/kidhome.html
       Database
778    LOLA                      List of lists annotated: a comparison of gene sets identified in    http://www.lola.gwu.edu/
                                 different microarray experiments
1092   M3D                       Many Microbe Microarrays Database                                   http://m3d.bu.edu/
  18   MAGEST                    Ascidian (Halocynthia roretzi) gene expression patterns             http://magest.hgc.jp/
 699   MAMEP                     Molecular Anatomy of the Mouse Embryo Project                       http://mamep.molgen.mpg.de/
 339   MEPD                      Gene expression in medaka (freshwater fish Oryzias latipes)         http://www.embl.de/mepd/
 541   NASCarrays                Nottingham Arabidopsis Stock Centre microarray database             http://affymetrix.arabidopsis.info
 709   OncoMine                  Cancer microarray data by gene or cancer type                       http://www.oncomine.org/
 558   PEPR                      Public Expression Profiling Resource                                http://pepr.cnmcresearch.org
 568   RefExA                    Reference database for human gene expression analysis               http://www.lsbm.org/site_e/database/index.html
 739   rOGED                     Rat ovarian gene expression database                                http://app.mc.uky.edu/kolab/rogedendo.aspx
 712   SAGEmap                    NCBI's resource for SAGE data from various organisms                  http://www.ncbi.nlm.nih.gov/SAGE
 742   SIEGE                      Smoking Induced Epithelial Gene Expression                            http://pulm.bumc.bu.edu/siegeDB
  22   Stanford Microarray DB     Raw and normalized data from microarray experiments                   http://genome-www.stanford.edu/microarray
1139   TMAD                       The Stanford Tissue Microarray Database                               http://tma.stanford.edu
 905   TmaDB                      Tissue microarray database                                            http://www.bioinformatics.leeds.ac.uk/tmadb/


       10. Proteomics Resources
 606   2D-PAGE                    Proteome database system for microbial research                       http://www.mpiib-berlin.mpg.de/2D-PAGE
1050   Biodefense Proteomics      Proteomics and host-pathogen interactions for biodefense-related      http://www.proteomicsresource.org/default.aspx
       Resource Center            microorganisms
731    DynaProt 2D                Proteome database of Lactococcus lactis                               http://www.wzw.tum.de/proteomik/lactis/
222    GELBANK                    2D gel electrophoresis patterns of proteins from complete microbial   http://gelbank.anl.gov
                                  genomes
950    MAPU                       Max-Planck Unified proteome database                                  http://www.mapuproteome.com
710    Open Proteomics DB         Mass-spectrometry-based proteomics data for human, yeast, E. coli     http://bioinformatics.icmb.utexas.edu/OPD/
                                  and Mycobacterium
850    PepSeeker                  Peptide identification and ion information from proteome              http://nwsr.bms.umist.ac.uk/cgi-
                                  experiments                                                           bin/pepseeker/pepseek.pl
851    PeptideAtlas               Peptides identified in LC-MS/MS proteomics experiments                http://www.peptideatlas.org
721    PlantMarkers               Database of predicted molecular markers from plants                   http://markers.btk.fi
857    PRIDE                      Proteomics peptide identification database                            http://www.ebi.ac.uk/pride/
225    SWISS-2DPAGE               Annotated 2D gel electrophoresis database                             http://www.expasy.org/ch2d/

       11. Other Molecular Biology Databases
 256   BioImage                   Database of multidimensional biological images                        http://www.bioimage.org/
 801   BioModels                  Published mathematical models of biological interest                  http://www.ebi.ac.uk/biomodels/
1171   Déjà vu                    Duplicate citations in the scientific literature                      http://spore.swmed.edu/dejavu/
 298   PubMed                     Citations and abstracts of biomedical literature                      http://pubmed.gov
 992   University of Pittsburgh   A collection of bioinformatic databases and software tools            http://www.hsls.pitt.edu/guides/genetics/obrc/
       Bioinformatics
       Resources Collection
701    MetaRouter                 Compounds and pathways related to bioremediation                      http://pdg.cnb.uam.es/MetaRouter
       11.1. Drugs and drug design
407    ANTIMIC                    Database of natural antimicrobial peptides                            http://research.i2r.a-
                                                                                                        star.edu.sg/Templar/DB/ANTIMIC/
 408   APD                        Antimicrobial Peptide Database                                        http://aps.unmc.edu/AP/main.php
1055   CEBS                       Database of toxicogenomics, microarray and proteomics data.           http://cebs.niehs.nih.gov
 443   DART                    Drug Adverse Reaction Targets                                          http://xin.cz3.nus.edu.sg/group/drt/dart.asp
 811   DrugBank                Combined information on drugs and drug targets                         http://redpoll.pharmacy.ualberta.ca/drugbank/
 819   GLIDA                   G-protein coupled receptors ligand database                            http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/
1002   PharmGED                PharmacoGenetic Effect Database                                        http://bidd.cz3.nus.edu.sg/phg/
 392   PharmGKB                Pharmacogenomics and Pharmacogenetics Knowledge Base                   http://www.pharmgkb.org
 741   Scorpion                Database of scorpion toxins                                            http://sdmc.i2r.a-star.edu.sg/scorpion/
 902   SuperDrug               2D and 3D chemical structures of various drugs                         http://bioinformatics.charite.de/superdrug
 903   SuperNatural            Natural compounds and their suppliers                                  http://bioinformatics.charite.de/supernatural
1136   SuperTarget             Drug-related information: medical indications, adverse drug effects,   http://insilico.charite.de/supertarget
                               drug metabolism and Gene Ontology terms of the target proteins
 315   TTD                     Therapeutic target database                                            http://xin.cz3.nus.edu.sg/group/cjttd/ttd.asp
1147   VIOLIN                  Vaccine Investigation and Online Information Network                   http://www.violinet.org
       11.2. Molecular probes and primers
781    AOBase                  Antisense oligonucleotide selection and design                         http://www.bioit.org.cn/ao/aobase
505    IMGT/PRIMER-DB          Immunogenetics oligonucleotide primer database                         http://imgt3d.igh.cnrs.fr/PrimerDB/Query_PrDB.pl
296    MPDB                    Molecular Probe Database                                               http://www.biotech.ist.unige.it/interlab/mpdb.html
728    Primer Studio           PCR primers for eukaryotic and prokaryotic genes                       http://bioinfo.ebc.ee/PrimerStudio/
390    probeBase               rRNA-targeted oligonucleotide probe sequences, DNA microarray          http://www.microbial-ecology.net/probebase
                               layouts, and associated information
 736   QPPD                    Quantitative PCR Primer Database                                       http://web.ncifcrf.gov/rtp/GEL/primerdb/default.asp
1008   qPrimerDepot            Quantitative real time PCR primers for human RefSeq sequences          http://primerdepot.nci.nih.gov/
 356   RTPrimerDB              Real-time PCR primer and probe sequences                               http://medgen.ugent.be/rtprimerdb/
 303   VirOligo                Virus-specific oligonucleotides for PCR and hybridization              http://viroligo.okstate.edu

       12. Organelle Databases
804    Chloroplast genome DB   Chloroplast genome database                                            http://chloroplast.cbio.psu.edu/
 74    GOBASE                  Organelle genome database                                              http://megasun.bch.umontreal.ca/gobase/gobase.ht
                                                                                                      ml
713    Organelle DB            Organelle proteins and subcellular structures                          http://organelledb.lsi.umich.edu/
601    Organelle genomes       NCBI's organelle genome resource                                       http://www.ncbi.nlm.nih.gov/genomes/ORGANELLE
                                                                                                      S/organelles.html
1001   PeroxisomeDB            Peroxisomal proteins, metabolic routes and diagnostic tools            http://www.peroxisomeDB.org
1115   Plant Organelles DB     Images and protocols for plant organelle research                      http://podb.nibb.ac.jp/Organellome
 722   PLprot                  Plastid protein database                                               http://www.plprot.ethz.ch/
       12.1. Mitochondrial Genes and Proteins
637    AMPDB                   Arabidopsis Mitochondrial Protein Database                             http://www.plantenergy.uwa.edu.au/applications/am
                                                                                                      pdb/index.html
 686   HMPD                     Human mitochondrial protein database                                   http://bioinfo.nist.gov/hmpd/
1174   HmtDB                    Human mitochondrial database                                           http://www.hmtdb.uniba.it/
 824   Human MtDB               Human mitochondrial genome database                                    http://www.genpat.uu.se/mtDB
  38   HvrBase++                Primate mitochondrial DNA control region sequences                     http://www.hvrbase.org
 894   MamMiBase                Mammalian mitochondrial genome database                                http://xavante.fmrp.usp.br/mammibase/
  64   Mitochondriome           Metazoan mitochondrial genes                                           http://www.ba.itb.cnr.it/mitochondriome/
  83   MitoDat                  Mitochondrial proteins (predominantly human)                           http://www-lecb.ncifcrf.gov/mitoDat/
  84   MITOMAP                  Human mitochondrial genome                                             http://www.mitomap.org/
1099   Mitome                   Comparative analysis of metazoan mitochondrial genomes                 http://www.mitome.info
  86   MITOP2                   Mitochondrial proteins, genes and diseases                             http://www.mitop2.de/
 532   MitoProteome             Experimentally described human mitochondrial proteins                  http://www.mitoproteome.org
 538   MPIMP db                 Mitochondrial protein import machinery of plants and yeast             http://www.plantenergy.uwa.edu.au/applications/mpi
                                                                                                       mp/
547    OGRe                     Organellar Genome Resource                                             http://ogre.mcmaster.ca

       13. Plant Databases

       13.1. General plant databases
599    BarleyBase               Expression profiling of plant genomes                                  http://www.barleybase.org/
982    Cereal Small RNA DB      Small RNAs expressed in rice and maize                                 http://sundarlab.ucdavis.edu/smrnas/
624    CR-EST                   Cropp ESTs: Barley, wheat, pea, and potato ESTs                        http://pgrc.ipk-gatersleben.de/cr-est/
888    DRASTIC                  Database resource for analysis of signal transduction in plant cells   http://www.drastic.org.uk
128    FLAGdb++                 Integrative database about plant genomes                               http://urgv.evry.inra.fr/projects/FLAGdb++/HTML/ind
                                                                                                       ex.shtml
 672   GabiPD                   Central database of the German Plant Genome Project                    http://gabi.rzpd.de
 675   GeneFarm                 Expert annotation of Arabidopsis gene and protein families             http://urgi.versailles.inra.fr/Genefarm/
 351   GénoPlante-Info          Plant genomic data from the Génoplante consortium                      http://www.genoplante.com/
 488   GrainGenes               Genes and phenotypes of wheat, barley, rye, triticale, oats            http://wheat.pw.usda.gov
 607   Gramene                  A resource for comparative grass genomics                              http://www.gramene.org
1095   MetaCrop                 Biochemical pathways and enzymes in crop plants                        http://metacrop.ipk-gatersleben.de
1029   MIPSPlantsDB             MIPS Plants Databases                                                  http://mips.gsf.de/proj/plant/jsf/
 581   openSputnik              Plant EST clustering and functional annotation                         No longer maintained
 999   PathoPlant               Signal transduction related to plant-pathogen interactions             http://www.pathoplant.de
 853   Phytome                  Comparative genomics of plant species                                  http://www.phytome.org
 956   Plant DNA C-values       Genome sizes of various plants and algae                               http://www.kew.org/genomesize/homepage.html
       Database
562    Plant Genome Central     NCBI’s portal for various large-scale plant genome and EST             http://www.ncbi.nlm.nih.gov/genomes/PLANTS/Plant
                                sequencing projects                                                    List.html
 843   Plant MPSS               Massively parallel signature sequencing of plant genes                 http://mpss.udel.edu
1116   Plant Stress-Responsi-   Stress-responsive gene in various plant species                        http://dayhoff.generationcp.org
       ve Gene Catalog
 355   PlantGDB                Plant genome database: Actively-transcribed plant genes              http://www.plantgdb.org/
1118   PlantTribes             Families of protein-coding genes from five sequenced plant species   http://www.floralgenome.org/tribe.php
 948   POGs/PlantRBP           Orthologous groups of RNA binding proteins in plants                 http://plantrbp.uoregon.edu
1119   PPDB                    Plant promoter database                                              http://ppdb.gene.nagoya-u.ac.jp
 578   SeedGenes               Genes essential for Arabidopsis development                          http://www.seedgenes.org/
 940   TIGR Plant Transcript   Transcript assemblies of plant EST and cDNA sequences                http://plantta.tigr.org
       Assembly database
313    TropGENE DB             Genes and genomes of sugarcane, banana, cocoa                        http://tropgenedb.cirad.fr/
 67    UK CropNet              Genome mapping in crop plants                                        http://ukcrop.net/
       13.2. Arabidopsis thaliana
636    AGNS                    Arabidopsis GeneNet supplementary                                    http://wwwmgs.bionet.nsc.ru/agns/
618    AGRIS                   Arabidopsis gene regulatory information server                       http://arabidopsis.med.ohio-state.edu
780    Arabidopsis MPSS        Arabidopsis gene expression detected by massively parallel           http://mpss.udel.edu/at/
                               signature sequencing
638    Arabidopsis Nucleolar   Comparative analysis of human and Arabidopsis nucleolar              http://bioinf.scri.sari.ac.uk/cgi-
       Protein Database        proteomes                                                            bin/atnopdb/proteome_comparison
640    Arabidopsis Small RNA   Arabidopsis Small RNA sequences                                      http://asrp.cgrb.oregonstate.edu/
       Project
880    ARTADEdb                Arabidopsis tiling-array-based detection of exons                    http://omicspace.riken.jp/ARTADE/
394    AtGDB                   Arabidopsis thaliana genome database                                 http://www.plantgdb.org/AtGDB
765    AthaMap                 Genome-wide map of putative transcription factor binding sites in    http://www.athamap.de/
                               Arabidopsis thaliana
934    ATTED-II                Coexpressed gene sets and gene regulators in Arabidopsis             http://www.atted.bio.titech.ac.jp/
610    Brassica BASC           Database for Brassica genomic research                               http://hornbill.cspp.latrobe.edu.au/cgi-
                                                                                                    binpub/brassica/index.pl
1054   CATdb                   Arabidopsis transcriptome data                                       http://urgv.evry.inra.fr/CATdb
 656   DATF                    Database of Arabidopsis transcription factors                        http://datf.cbi.pku.edu.cn
 935   GABI-Kat                Flanking sequence tags for T-DNA insertions in Arabidopsis           http://www.GABI-Kat.de
1081   GreenPhylDB             Comparative genomics of rice and Arabidopsis thaliana                http://greenphyl.cirad.fr
 527   MAtDB                   MIPS Arabidopsis thaliana database                                   http://mips.gsf.de/proj/thal/db
1004   PlantQTL-GE             Quantitative trait locus analysis in Arabidopsis and rice            http://www.scbit.org/qtl2gene
 738   RARGE                   RIKEN Arabidopsis genome encyclopedia: cDNAs, mutants and            http://rarge.gsc.riken.jp/
                               microarray data
 97    TAIR                    The Arabidopsis information resource                                 http://www.arabidopsis.org/
627    WAtDB                   Wageningen Arabidopsis thaliana Database                             No longer maintained
       13.3. Rice
418    BGI-RISe                Beijing Genomics Institute Rice Information System                   http://rise.genomics.org.cn/
1156   DRTF                   Database of Rice Transcription Factors                             http://drtf.cbi.pku.edu.cn/
  79   INE                    Integrated rice genome explorer                                    http://rgp.dna.affrc.go.jp/giot/INE.html
 353   IRIS -                 International Rice Information System                              http://www.iris.irri.org
 536   MOsDB                  MIPS Oryza sativa database                                         http://mips.gsf.de/proj/plant/jsf/rice/index.jsp
 848   OryGenesDB             Rice genes, T-DNA and Ds flanking sequence tags                    http://orygenesdb.cirad.fr/
 628   Oryza Tag Line         T-DNA insertion mutants of rice                                    http://urgi.versailles.inra.fr/OryzaTagLine/
  90   Oryzabase              Rice genetics and genomics                                         http://www.shigen.nig.ac.jp/rice/oryzabase/
 860   RAP-DB                 Rice annotation project database                                   http://rapdb.dna.affrc.go.jp/
 737   Rice Annotation DB     Contig data for manual annotation of rice genome                   http://golgi.gs.dna.affrc.go.jp/SY-1102/rad/index.html
 861   Rice Mutant Database   Rice mutant database                                               http://rmd.ncpgr.cn/
 569   Rice Pipeline          Unification tool for rice databases                                http://cdna01.dna.affrc.go.jp/PIPE
 572   Rice Proteome DB       Rice proteome database                                             http://gene64.dna.affrc.go.jp/RPD/main_en.html
 336   RiceGAAS               Rice genome automated annotation system                            http://ricegaas.dna.affrc.go.jp/
       13.4. Other plants
 971   ForestTreeDB           Annotated ESTs from diverse organs of conifer and poplar trees     http://foresttree.org/ftdb
1078   Genome Database for    Genetics and genomics data on apple, cherry, peach, pear,          http://www.bioinfo.wsu.edu/gdr/
       Rosaceae               raspberry, rose and strawberry
80     Legume Information     Legume information server (formerly Medicago genome initiative):   http://www.comparative-legumes.org/
       System                 ESTs, gene expression and proteomic data
 526   MaizeGDB               Maize genetics and genomics database                               http://www.maizegdb.org
1159   MedicCyc               Biochemical pathways in Medicago truncatula                        http://www.noble.org/mediccyc/
 539   MtDB                   <I>Medicago trunculata</I> Database                                http://www.medicago.org/MtDB
 921   NRESTdb                Natural Rubber EST Database                                        http://genome.ukm.my/nrestdb/
 849   Panzea                 Maize genome project data                                          http://www.panzea.org
 620   PoMaMo                 Potato Maps and More                                               https://gabi.rzpd.de/PoMaMo.html
 766   SGMD                   Soybean genomics and microarray database                           http://psi081.ba.ars.usda.gov/SGMD/default.htm
1132   Shanghai Rapeseed      Seed development and fatty acid metabolism of oilseed crops        http://rapeseed.plantsignal.cn
       Database
 919   SoyBase                Genetic, genomic and phenotypic information about soybean          http://soybase.org
 870   SoyGD                  Soybean genome database                                            http://soybeangenome.siu.edu
 872   TED                    Tomato expression database                                         http://ted.bti.cornell.edu
 874   TIGR Maize database    Maize genome sequencing consortium site                            http://maize.tigr.org
1016   TomatEST DB            EST collection from multiple tomato species                        http://biosrv.cab.unina.it
          14. Immunological Databases
    799   AntiJen                  Quantitative binding data for peptides and proteins of                 http://www.jenner.ac.uk/AntiJen
                                   immunological interest
    642   BCIpep                   Database of B-cell epitopes                                            http://bioinformatics.uams.edu/mirror/bcipep/
    604   dbMHC                    Genetic and clinical database of the human MHC                         http://www.ncbi.nlm.nih.gov/mhc/
    813   Epitome                  Antigenic epitopes in proteins and antibodies that bind them           http://predictprotein.org/AifoEpi/
    150   FIMM                     Functional molecular immunology data                                   http://research.i2r.a-star.edu.sg/fimm
    682   Haptendb                 Curated database of hapten molecules                                   http://www.imtech.res.in/raghava/haptendb/
    172   IMGT                     International immunogenetics information system:                       http://imgt.cines.fr
                                   Immunoglobulins, T cell receptors, MHC, and RPI
    503   IMGT/GENE-DB             Vertebrate immunoglobulin and T cell receptor genes                    http://imgt.cines.fr/cgi-bin/GENElect.jv
    173   IMGT/HLA                 Polymorphism of human MHC and related genes                            http://www.ebi.ac.uk/imgt/hla/
    504   IMGT/LIGM-DB             Immunoglobulin, T cell receptor and MHC nucleotide sequences           http://imgt.cines.fr/cgi-bin/IMGTlect.jv
                                   from human and other vertebrates
    779   Immune epitope DB        Antibody and T cell epitopes for primates, rodents, and other          http://www.immuneepitope.org/
                                   animals
    367   IPD                      Immuno Polymorphism Database                                           http://www.ebi.ac.uk/ipd/
    692   IPD-ESTDAB               Immunologically characterised melanoma cell lines                      http://www.ebi.ac.uk/ipd/
    693   IPD-HPA                  Human platelet antigens                                                http://www.ebi.ac.uk/ipd/
    694   IPD-KIR                  Killer-cell Immunoglobulin-like Receptors                              http://www.ebi.ac.uk/ipd/
    691   IPD-MHC                  Sequences of the major histocompatibility complex                      http://www.ebi.ac.uk/ipd/mhc
    361   JenPep                   Quantitative binding data for peptides and proteins of                 Superseded by AntiJen, no. 799
                                   immunological interest
 702      MHCBN                    Database of MHC binding and non-binding peptides                       http://www.imtech.res.in/raghava/mhcbn/
 181      MHCPEP                   MHC-binding peptides                                                   http://bio.dfci.harvard.edu/DFRMLI/
1101      MUGEN Mouse DB           Murine models of immune processes and immunological diseases           http://www.mugen-noe.org/database/
 967      SuperHapten              A comprehensive database for small immunogenic compounds               http://bioinformatics.charite.de/superhapten
 621      VBASE2                   Variable genes from the Ig loci of human and mouse                     http://www.vbase2.org/


a
 – Each database is shown in the list only once. In another version of this list, available at the NAR web site http://www.oxfordjournals.org/nar/database/a/, a
database can be listed under two (sub)categories.
b
 – Accession number of the database in the on-line list; can be used to view the database summary. For example,
http://www.oxfordjournals.org/nar/database/summary/1 shows the summary for DDBJ.
c
    – In some database names, the word "database" is abbreviated as “DB”.

								
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