Home LiteratureArticle Details
PMID: 18086701 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

The UCSC Genome Browser Database: 2008 update.

Nucleic acids research ·Vol. 36 ·No. Database issue ·2008-01-00 ·Pages D773-9

Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F, Kober KM, Miller W, Pedersen JS, Pohl A, Raney BJ, Rhead B, Rosenbloom KR, Smith KE, Stanke M, Thakkapallayil A, Trumbower H, Wang T, Zweig AS, Haussler D, Kent WJ

Abstract

The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrate and 21 invertebrate species as of September 2007. For each assembly, the GBD contains a collection of annotation data aligned to the genomic sequence. Highlights of this year's additions include a 28-species human-based vertebrate conservation annotation, an enhanced UCSC Genes set, and more human variation, MGC, and ENCODE data. The database is optimized for fast interactive performance with a set of web-based tools that may be used to view, manipulate, filter and download the annotation data. New toolset features include the Genome Graphs tool for displaying genome-wide data sets, session saving and sharing, better custom track management, expanded Genome Browser configuration options and a Genome Browser wiki site. The downloadable GBD data, the companion Genome Browser toolset and links to documentation and related information can be found at: http://genome.ucsc.edu/.

MeSH Terms
Animals Computer Graphics Databases, Nucleic Acid Genetic Variation Genomics Humans Internet Invertebrates/genetics Sequence Alignment User-Computer Interface Vertebrates/genetics
Authors & Affiliations
25 authors, click to expand affiliations / ORCID
Karolchik D
Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA. [email protected]
Kuhn R M
Baertsch R
Barber G P
Clawson H
Diekhans M
Giardine B
Harte R A
Hinrichs A S
Hsu F
Kober K M
Miller W
Pedersen J S
Pohl A
Raney B J
Rhead B
Rosenbloom K R
Smith K E
Stanke M
Thakkapallayil A
Trumbower H
Wang T
Zweig A S
Haussler D
Kent W J
References (40)
40 references, click to expand
  1. Exploring relationships and mining data with the UCSC Gene Sorter.
    Genome Res. 2005 May;15(5):737-41 PMID: 15867434
  2. Database resources of the National Center for Biotechnology Information.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D5-12 PMID: 17170002
  3. dbSNP: the NCBI database of genetic variation.
    Nucleic Acids Res. 2001 Jan 1;29(1):308-11 PMID: 11125122
  4. Identification and analysis of alternative splicing events conserved in human and mouse.
    Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):2850-5 PMID: 15708978
  5. A human protein-protein interaction network: a resource for annotating the proteome.
    Cell. 2005 Sep 23;122(6):957-68 PMID: 16169070
  6. A haplotype map of the human genome.
    Nature. 2005 Oct 27;437(7063):1299-320 PMID: 16255080
  7. Large-scale copy number polymorphism in the human genome.
    Science. 2004 Jul 23;305(5683):525-8 PMID: 15273396
  8. Genome and genetic resources from the Cancer Genome Anatomy Project.
    Hum Mol Genet. 2001 Apr;10(7):663-7 PMID: 11257097
  9. The human genome browser at UCSC.
    Genome Res. 2002 Jun;12(6):996-1006 PMID: 12045153
  10. A genome annotation-driven approach to cloning the human ORFeome.
    Genome Biol. 2004;5(10):R84 PMID: 15461802
  11. Human protein reference database--2006 update.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D411-4 PMID: 16381900
  12. Detection of large-scale variation in the human genome.
    Nat Genet. 2004 Sep;36(9):949-51 PMID: 15286789
  13. Towards a proteome-scale map of the human protein-protein interaction network.
    Nature. 2005 Oct 20;437(7062):1173-8 PMID: 16189514
  14. A high-resolution survey of deletion polymorphism in the human genome.
    Nat Genet. 2006 Jan;38(1):75-81 PMID: 16327808
  15. Global variation in copy number in the human genome.
    Nature. 2006 Nov 23;444(7118):444-54 PMID: 17122850
  16. The ENCODE Project at UC Santa Cruz.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D663-7 PMID: 17166863
  17. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
    Nature. 2007 Jun 14;447(7146):799-816 PMID: 17571346
  18. The UCSC Known Genes.
    Bioinformatics. 2006 May 1;22(9):1036-46 PMID: 16500937
  19. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D61-5 PMID: 17130148
  20. Mutant-specific gene programs in the zebrafish.
    Blood. 2005 Jul 15;106(2):521-30 PMID: 15827125
  21. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
    Genome Res. 2005 Aug;15(8):1034-50 PMID: 16024819
  22. Aligning multiple genomic sequences with the threaded blockset aligner.
    Genome Res. 2004 Apr;14(4):708-15 PMID: 15060014
  23. Thousands of human mobile element fragments undergo strong purifying selection near developmental genes.
    Proc Natl Acad Sci U S A. 2007 May 8;104(19):8005-10 PMID: 17463089
  24. GenBank.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D21-5 PMID: 17202161
  25. Structural variation in the human genome.
    Nat Rev Genet. 2006 Feb;7(2):85-97 PMID: 16418744
  26. Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome.
    Am J Hum Genet. 2006 Aug;79(2):275-90 PMID: 16826518
  27. The Universal Protein Resource (UniProt).
    Nucleic Acids Res. 2007 Jan;35(Database issue):D193-7 PMID: 17142230
  28. Common deletion polymorphisms in the human genome.
    Nat Genet. 2006 Jan;38(1):86-92 PMID: 16468122
  29. The UCSC Table Browser data retrieval tool.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6 PMID: 14681465
  30. ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation.
    Bioinformatics. 2006 Mar 1;22(5):637-40 PMID: 16397004
  31. Serial analysis of gene expression.
    Science. 1995 Oct 20;270(5235):484-7 PMID: 7570003
  32. Common deletions and SNPs are in linkage disequilibrium in the human genome.
    Nat Genet. 2006 Jan;38(1):82-5 PMID: 16327809
  33. The UCSC genome browser database: update 2007.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D668-73 PMID: 17142222
  34. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
    Genome Res. 2004 Oct;14(10B):2121-7 PMID: 15489334
  35. Segmental duplications and copy-number variation in the human genome.
    Am J Hum Genet. 2005 Jul;77(1):78-88 PMID: 15918152
  36. BLAT--the BLAST-like alignment tool.
    Genome Res. 2002 Apr;12(4):656-64 PMID: 11932250
  37. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
    Nature. 2007 Jun 7;447(7145):661-78 PMID: 17554300
  38. The UCSC Proteome Browser.
    Nucleic Acids Res. 2005 Jan 1;33(Database issue):D454-8 PMID: 15608236
  39. Ensembl 2007.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D610-7 PMID: 17148474
  40. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution.
    Science. 2005 May 20;308(5725):1149-54 PMID: 15790807
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkm966
Email
[email protected]
Published
2008-01-00
Epub
2007-00-17
Pages
D773-9
Language
English
Region
England
NLM ID
0411011
PMCID
PMC2238835
Subset
IM
Grants
NHGRI NIH HHS · P41 HG002371 · United States
NHGRI NIH HHS · 2 P41 HG002371-06 · United States
NHGRI NIH HHS · 3 P41 HG002371-06S1 · United States
NCI NIH HHS · N01CO12400 · United States
NCI NIH HHS · N01-CO-12400 · United States
NHGRI NIH HHS · U54 HG004555 · United States
External Links
PubMed source DOI: 10.1093/nar/gkm966 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2