5. Genomics Databases (non human)

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copied from Nucleic Acids Research, 2005, Vol. 33, Database issue (link directs to table of contents with many original papers on the below mentioned databases)
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No.^b

Database_name_____

Full_name_and/or_description_______________________

URL

5. Genomics Databases (non-human)

5.1. Genome annotation terms, ontologies and nomenclature

73 Genew Human gene nomenclature: approved gene symbols http://www.gene.ucl.ac.uk/nomenclature

487 GO Gene ontology consortium database http://www.geneontology.org/

389 GOA EBI's gene ontology annotation project http://www.ebi.ac.uk/GOA

513 IUBMB Nomenclature database Nomenclature of enzymes, membrane transporters, electron transport proteins and other proteins http://www.chem.qmul.ac.uk/iubmb

514 IUPAC Nomenclature database Nomenclature of biochemical and organic compounds approved by the IUBMB-IUPAC Joint Commission http://www.chem.qmul.ac.uk/iupac

515 IUPHAR-RD The International Union of Pharmacology recommendations on receptor nomenclature and drug classification http://www.iuphar-db.org/iuphar-rd/

552 PANTHER Gene products organized by biological function http://panther.celera.com/

317 UMLS Unified medical language system http://umlsks.nlm.nih.gov/

5.1.1. Taxonomy and Identification

78 ICB gyrB database for identification and classification of bacteria http://seasquirt.mbio.co.jp/icb/index.php

297 NCBI Taxonomy Names of all organisms represented in GenBank http://www.ncbi.nlm.nih.gov/Taxonomy/

608 PANDIT Protein and associated nucleotide domains with inferred trees http://www.ebi.ac.uk/goldman-srv/pandit/

299 RIDOM rRNA-based differentiation of medical microorganisms http://www.ridom-rdna.de/

243 RDP-II Ribosomal database project http://rdp.cme.msu.edu

301 Tree of Life Information on phylogeny and biodiversity http://phylogeny.arizona.edu/tree/phylogeny.html

5.2. General genomics databases

7 COG Clusters of orthologous groups of proteins http://www.ncbi.nlm.nih.gov/COG

650 COGENT Complete genome tracking: predicted peptides from fully sequenced genomes http://maine.ebi.ac.uk:8000/services/cogent/

337 CORG Comparative regulatory genomics: conserved non-coding sequence blocks http://corg.molgen.mpg.de/

445 DEG Database of essential genes from bacteria and yeast http://tubic.tju.edu.cn/deg

451 EBI Genomes EBI's collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes http://www.ebi.ac.uk/genomes

453 EGO Eukaryotic gene orthologs: orthologous DNA sequences in the TIGR gene indices http://www.tigr.org/tdb/tgi/ego/

70 EMGlib Enhanced microbial genomes library: completely sequenced genomes of unicellular organisms http://pbil.univ-lyon1.fr/emglib/emglib.html

458 Entrez Genomes NCBI's collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome

461 ERGOLight Integrated biochemical data on nine bacterial genomes: publicly available portion of the ERGO database http://www.ergo-light.com/ERGO

470 FusionDB Database of bacterial and archaeal gene fusion events http://igs-server.cnrs-mrs.fr/FusionDB

611 Genome Atlas DNA structural properties of sequenced genomes http://www.cbs.dtu.dk/services/GenomeAtlas/

484 Genome Information Broker DDBJ's collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes http://gib.genes.nig.ac.jp

678 Genome Reviews Integrated view of complete genomes http://www.ebi.ac.uk/GenomeReviews/

75 GOLD Genomes online database: a listing of completed and ongoing genome projects http://www.genomesonline.org/

352 HGT-DB Putative horizontally transferred genes in prokaryotic genomes http://www.fut.es/~debb/HGT/

223 Integr8 Functional classification of proteins in whole genomes http://www.ebi.ac.uk/integr8/

112 KEGG Kyoto encyclopedia of genes and genomes: integrated suite of databases on genes, proteins and metabolic pathways http://www.genome.jp/kegg

528 MBGD Microbial genome database for comparative analysis http://mbgd.genome.ad.jp/

549 ORFanage Database of orphan ORFs (ORFs with no homologs) in complete microbial genomes http://www.cs.bgu.ac.il/~nomsiew/ORFans

551 PACRAT Archaeal and bacterial intergenic sequence features http://www.biosci.ohio-tate.edu/~pacrat

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/

99 TIGR Microbial Database Lists of completed and ongoing genome projects with links to complete genome sequences http://www.tigr.org/tdb/mdb/mdbcomplete.html

66 TIGR Comprehensive Microbial Resource Various data on complete microbial genomes: uniform annotation, properties of DNA and predicted proteins http://www.tigr.org/CMR

311 TransportDB Predicted membrane transporters in complete genomes, classified according to the TC classification system http://www.membranetransport.org/

118 WIT3 What is there? Metabolic reconstruction for completely sequenced microbial genomes http://www-wit.mcs.anl.gov/wit3/

5.3. Organism-specific databases

5.3.1. Viruses

473 HCVDB The hepatitis C virus database http://hepatitis.ibcp.fr/

497 HIV Drug Resistance Database HIV mutations that confer resistance to anti-HIV drugs http://resdb.lanl.gov/Resist_DB/default.htm

168 HIV Molecular Immunology Database HIV epitopes http://hiv-web.lanl.gov/immunology/

365 HIV RT and Protease Sequence Database HIV reverse transcriptase and protease sequences http://hivdb.stanford.edu/

602 NCBI Viral Genomes Viral genome resource at NCBI http://www.ncbi.nlm.nih.gov/genomes/VIRUSES/viruses.html

725 Poxvirus.org Poxvirus genomic sequences and gene annotation http://www.poxvirus.org/

750 T4-like genome database 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/VIDA.html

761 VIPER Virus particle explorer: virus capsid structures http://mmtsb.scripps.edu/viper

303 VirOligo Virus-specific oligonucleotides for PCR and hybridization http://viroligo.okstate.edu/

5.3.2. Prokaryotes

641 BacMap Picture atlas of annotated bacterial genomes http://wishart.biology.ualberta.ca/BacMap

614 MetaGrowth Growth requirements of bacterial pathogens http://igs-server.cnrs-mrs.fr/axenic/

720 PGTdb Prokaryotic growth temperature database http://pgtdb.csie.ncu.edu.tw/

5.3.2.1. Escherichia coli

415 ASAP A systematic annotation package for community analysis of E.coli and related genomes https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm

428 CyberCell database A collection of data on E.coli K12 intended for mathematical modeling to simulate the bacterial cell http://redpoll.pharmacy.ualberta.ca/CCDB

436 coliBase A database for E.coli, Salmonella and Shigella http://colibase.bham.ac.uk/

437 Colibri E.coli genome database at Institut Pasteur http://genolist.pasteur.fr/Colibri/

623 EchoBASE Post-genomic studies of Escherichia coli http://www.ecoli-york.org/

462 Essential genes in E.coli First results of an E.coli gene deletion project http://www.genome.wisc.edu/resources/essential.htm

482 GenoBase E.coli genome database at Nara Institute http://ecoli.aist-nara.ac.jp/

165 GenProtEC E.coli K12 genome and proteome database http://genprotec.mbl.edu

555 PEC Profiling of E.coli chromosome http://shigen.lab.nig.ac.jp/ecoli/pec

108 EcoCyc E.coli K12 genes, metabolic pathways, transporters and gene regulation http://ecocyc.org/

69 EcoGene Sequence and literature data on E.coli genes and proteins http://bmb.med.miami.edu/EcoGene/EcoWeb/

116 RegulonDB Transcriptional regulation and operon organization in E.coli http://www.cifn.unam.mx/Computational_Genomics/regulondb/

5.3.2.2. Bacillus subtilis

424 BSORF Bacillus subtilis genome database at Kyoto U. http://bacillus.genome.ad.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/

5.3.2.3. Other bacteria

420 BioCyc Pathway/genome databases for many bacteria http://biocyc.org/

426 CampyDB Database for Campylobacter genome analysis http://campy.bham.ac.uk/

433 ClostriDB Finished and unfinished genomes of Clostridium spp. http://clostri.bham.ac.uk/

648 CIDB Chlamydia Interactive Database: gene expression data http://www.it.deakin.edu.au/CIDB

68 CyanoBase Cyanobacterial genomes http://www.kazusa.or.jp/cyano

521 LeptoList Leptospira interrogans genome http://bioinfo.hku.hk/LeptoList

534 MolliGen Genomic data on mollicutes http://cbi.labri.fr/outils/molligen/

733 PseudoCAP Pseudomonas aeruginosa genome database and community annotation project http://www.pseudomonas.com/

94 RsGDB Rhodobacter sphaeroides genome http://www.hgsc.bcm.tmc.edu/projects/microbial/Rsphaeroides/

762 VirFact Bacterial virulence factors and pathogenicity islands http://virfact.burnham.org/

760 Virulence Factors Reference database for microbial virulence factors http://zdsys.chgb.org.cn/VFs/main.htm

5.3.3. Unicellular eukaryotes

409 ApiEST-DB EST sequences from various Apicomplexan parasites http://www.cbil.upenn.edu/paradbs-servlet

439 CryptoDB Cryptosporidium parvum genome database http://cryptodb.org/

662 Diatom EST Database ESTs from two diatom algae, Thalassiosira pseudonana and Phaeodactylum tricornutum http://avesthagen.sznbowler.com/

446 DictyBase Universal resource for Dictyostelium discoideum http://dictybase.org/

72 Full-Malaria Full-length cDNA library from erythrocytic-stage Plasmodium falciparum http://fullmal.ims.u-tokyo.ac.jp/

328 GeneDB Curated database for various Sanger-sequenced genomes http://www.genedb.org/

698 LumbriBASE ESTs of the earthworm Lumbricus rubellus http://www.earthworms.org/

91 PlasmoDB Plasmodium genome database http://plasmodb.org/

586 TcruziDB Trypanosoma cruzi genome database http://tcruzidb.org/

359 ToxoDB Toxoplasma gondii genome database http://toxodb.org/

5.3.4. Fungi

5.3.4.1. 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

730 PROPHECY Profiling of phenotypic characteristics in yeast http://prophecy.lundberg.gu.se/

576 SCMD Saccharomyces cerevisiae morphological database: micrographs of budding yeast mutants http://yeast.gi.k.u-tokyo.ac.jp/

577 SCPD Saccharomyces cerevisiae promoter database http://cgsigma.cshl.org/jian

357 SGD Saccharomyces genome database http://www.yeastgenome.org/

25 TRIPLES Transposon-insertion phenotypes, localization and expression in Saccharomyces http://ygac.med.yale.edu/triples/

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

254 Yeast snoRNA Database Yeast small nucleolar RNAs http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html

307 yMGV Yeast microarray global viewer http://www.transcriptome.ens.fr/ymgv/

763 YRC PDR Yeast resource center public data repository http://www.yeastrc.org/pdr/

5.3.4.2. 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

533 MNCDB MIPS Neurospora crassa database http://mips.gsf.de/proj/neurospora/

708 OGD Oomycete Genomics Database: ESTs and annotation http://www.oomycete.net/

98 Phytophthora Functional Genomics Database ESTs and expression data from P.infestans and P.sojae http://www.pfgd.org/pfgd/

5.3.5. Invertebrates

5.3.5.1. 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/

100 WILMA C.elegans annotation database http://www.came.sbg.ac.at/wilma/

304 WorfDB C.elegans ORFeome http://worfdb.dfci.harvard.edu/

51 WormBase Data repository for C.elegans and C.briggsae: curated genome annotation, genetic and physical maps, pathways http://www.wormbase.org/

5.3.5.2. Drosophila melanogaster

71 FlyBase Drosophila sequences and genomic information http://flybase.bio.indiana.edu/

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/

467 FlyTrap Drosophila mutants created using GFP protein trap strategy http://flytrap.med.yale.edu/

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/

774 DPDB Drosophila polymorphism database http://dpdb.uab.es/

449 Drosophila microarray project Data and tools for Drosophila gene expression studies http://www.flyarrays.com/fruitfly

509 InterActive Fly Drosophila genes and their roles in development http://sdb.bio.purdue.edu/fly/aimain/1aahome.htm

5.3.5.3. Other invertebrates

410 AppaDB A 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/

649 Ciliate IES-MDS Db Macro- and micronuclear genes in spirotrichous ciliates http://oxytricha.princeton.edu/dimorphism/database.htm

434 CnidBase Cnidarian evolution and gene expression database http://cnidbase.bu.edu/

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://bighost.area.ba.cnr.it/PPNEMA/

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://www.cdfd.org.in/silksatdb/

747 SpodoBase Genomics of the butterfly Spodoptera frugiperda http://bioweb.ensam.inra.fr/spodobase/

^a Each database is shown in the list only once, often in a category that was arbitrarily chosen among two or three appropriate ones. In the online version of this list at the NAR website (http://nar.oupjournals.org/), a database can be listed under two categories.

^b Accession number of the database in the online list; can be used to view the database summary, e.g. http://www3.oup.co.uk/nar/database/summary/1 shows the summary for DDBJ.