7. Human and other Vertebrate Genomes

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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

7. Human and other Vertebrate Genomes

7.1. Model organisms, comparative genomics

63 ACeDB C.elegans, S.pombe and human genomic information http://www.acedb.org/

26 AllGenes Human and mouse gene, transcript and protein annotation http://www.allgenes.org/

65 ArkDB Genome databases for farm and other animals http://www.thearkdb.org/

647 ChickVD Sequence variation in the chicken genome http://chicken.genomics.org.cn/

286 Cre Transgenic Database Cre transgenic mouse lines with links to publications http://www.mshri.on.ca/nagy/

660 DED Database of evolutionary distances http://warta.bio.psu.edu/DED/

27 Ensembl Annotated information on eukaryotic genomes http://www.ensembl.org/

465 FANTOM Functional annotation of mouse full-length cDNA clones http://fantom2.gsc.riken.go.jp

468 FREP Functional repeats in mouse cDNAs http://facts.gsc.riken.go.jp/FREP/

673 GALA Genomic alignment, annotation and experimental results http://gala.cse.psu.edu/

347 GenetPig Genes controlling economic traits in pig http://www.infobiogen.fr/services/Genetpig

605 HomoloGene Automatically detected homologous genes in complete eukaryotic genomes http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene

690 Inparanoid A database of eukaryotic orthologs http://inparanoid.cgb.ki.se/

696 IPI International protein index: non-redundant sets of human, mouse and rat proteins http://www.ebi.ac.uk/IPI

777 KaryotypeDB Karyotype and chromosome information for animal and plant species http://www.nenno.it/karyotypedb/

400 KOG Eukaryotic orthologous groups of proteins http://www.ncbi.nlm.nih.gov/COG/new/shokog.cgi

87 Mouse Genome Informatics Formerly mouse genome database http://www.informatics.jax.org/

540 MTID Mouse transposon insertion database http://mouse.ccgb.umn.edu/transposon/

703 NegProt Negative Proteome: a tool for comparison of complete proteomes http://superfly.ucsd.edu/negprot

556 PEDE Pig EST data explorer: full-length cDNAs and ESTs http://pede.gene.staff.or.jp/

665 PhenomicDB Comparison of phenotypes of orthologous genes in human and model organisms http://www.phenomicdb.de/

724 Polymorphix A database of sequence polymorphisms http://pbil.univ-lyon1.fr/polymorphix/query.php

93 Rat Genome Database Rat genetic and genomic data http://rgd.mcw.edu/

625 RatMap Rat genome tools and data http://ratmap.org/

751 TAED The adaptive evolution database: a phylogeny-based tool for comparative genomics http://www.bioinfo.no/tools/TAED

5 TIGR Gene Indices Organism-specific databases of EST and gene sequences http://www.tigr.org/tdb/tgi.shtml

6 UniGene Unified clusters of ESTs and full-length mRNA sequences http://www.ncbi.nlm.nih.gov/UniGene/

319 UniSTS Unified view of sequence tagged sites with mapping data http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unists

783 VEGA Vertebrate genome annotation: a repository for manual annotation of finished vertebrate genome sequences http://vega.sanger.ac.uk/

101 ZFIN Zebrafish information network http://zfin.org/

7.2. Human genome databases, maps and viewers

27 Ensembl Annotated information on eukaryotic genomes http://www.ensembl.org/

404 AluGene Complete Alu map in the human genome http://alugene.tau.ac.il/

349 CroW 21 Human chromosome 21 database http://bioinfo.weizmann.ac.il/crow21/

55 GB4-RH Genebridge4 human radiation hybrid maps http://www.sanger.ac.uk/Software/RHserver/RHserver.shtml

56 GDB Human genes and genomic maps http://www.gdb.org/

57 GenAtlas Human genes, markers and phenotypes http://www.genatlas.org/

350 GeneCards Integrated database of human genes, maps, proteins and diseases http://bioinfo.weizmann.ac.il/cards/

348 GeneLoc Gene location database (formerly UDB—Unified database for human genome mapping) http://genecards.weizmann.ac.il/geneloc/

327 GeneNest Gene indices of human, mouse, zebrafish, etc. http://genenest.molgen.mpg.de/

59 GenMapDB Mapped human BAC clones http://genomics.med.upenn.edu/genmapdb

35 Gene Resource Locator Alignment of ESTs with finished human sequence http://grl.gi.k.u-tokyo.ac.jp/

324 HOWDY Human organized whole genome database http://www-alis.tokyo.jst.go.jp/HOWDY/

60 HuGeMap Human genome genetic and physical map data http://www.infobiogen.fr/services/Hugemap

77 Human BAC Ends Non-redundant human BAC end sequences http://www.tigr.org/tdb/humgen/bac_end_search/bac_end_intro.html

597 Human Genome Segmental Duplication Database Segmental duplications in the human genome http://projects.tcag.ca/humandup

61 IXDB Physical maps of human chromosome X http://ixdb.mpimg-berlin-dahlem.mpg.de/

697 L1Base Functional annotation and prediction of LINE-1 elements http://line1.molgen.mpg.de/

54 Map Viewer Display of genomic information by chromosomal position http://www.ncbi.nlm.nih.gov/mapview/

600 MGC Mammalian genome collection: full-length ORFs for human, mouse and rat genes http://mgc.nci.nih.gov/

391 NCBI RefSeq Non-redundant collection of naturally occurring biological molecules http://www.ncbi.nlm.nih.gov/RefSeq/

553 ParaDB Paralogy mapping in human genomes http://abi.marseille.inserm.fr/paradb/

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/

4 STACK Sequence tag alignment and consensus knowledgebase http://www.sanbi.ac.za/Dbases.html

596 The Chromosome 7 Annotation Project A comprehensive description of human chromosome 7 http://www.chr7.org/

684 TRBase Tandem repeats in the human genome http://bioinfo.ex.ac.uk/trbase

316 UCSC Genome Browser Genome assemblies and annotation http://genome.ucsc.edu/

7.3. Human proteins

685 H-InvDB Full-length human cDNA clones http://www.h-invitational.jp/

499 HPMR Human plasma membrane receptome: sequences, literature and expression data http://receptome.stanford.edu/

500 HPRD Human protein reference database: domain architecture, post-translational modifications and disease association http://www.hprd.org

37 HUNT Human novel transcripts: annotated full-length cDNAs http://www.hri.co.jp/HUNT

171 HUGE Human unidentified gene-encoded large (>50 kDa) protein and cDNA sequences http://www.kazusa.or.jp/huge

522 LIFEdb Localization, interaction and functions of human proteins http://www.dkfz.de/LIFEdb

312 trome, trEST and trGEN: Databases of predicted human protein sequences ftp://ftp.isrec.isb-sib.ch/pub/databases/

^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.