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PMID: 17142222 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

The UCSC genome browser database: update 2007.

Nucleic acids research ·Vol. 35 ·No. Database issue ·2007-01-00 ·Pages D668-73

Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, Thakkapallayil A, Sugnet CW, Stanke M, Smith KE, Siepel A, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pedersen JS, Hsu F, Hinrichs AS, Harte RA, Diekhans M, Clawson H, Bejerano G, Barber GP, Baertsch R, Haussler D, Kent WJ

Abstract

The University of California, Santa Cruz Genome Browser Database contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up to a full chromosome and includes assembly data, genes and gene predictions, mRNA and EST alignments, and comparative genomics, regulation, expression and variation data. The database is optimized for fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. In the past year, 22 new assemblies and several new sets of human variation annotation have been released. New features include VisiGene, a fully integrated in situ hybridization image browser; phyloGif, for drawing evolutionary tree diagrams; a redesigned Custom Track feature; an expanded SNP annotation track; and many new display options. The Genome Browser, other tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.

MeSH Terms
Animals Base Sequence Cattle Computer Graphics Conserved Sequence Databases, Genetic Genome, Human Genomics Humans Internet Linkage Disequilibrium Mice Open Reading Frames Polymorphism, Single Nucleotide Rats Regulatory Sequences, Nucleic Acid User-Computer Interface
Authors & Affiliations
25 authors, click to expand affiliations / ORCID
Kuhn R M
Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA. kuhn@soe.ucsc.edu
Karolchik D
Zweig A S
Trumbower H
Thomas D J
Thakkapallayil A
Sugnet C W
Stanke M
Smith K E
Siepel A
Rosenbloom K R
Rhead B
Raney B J
Pohl A
Pedersen J S
Hsu F
Hinrichs A S
Harte R A
Diekhans M
Clawson H
Bejerano G
Barber G P
Baertsch R
Haussler D
Kent W J
References (37)
37 references, click to expand
  1. dbSNP: a database of single nucleotide polymorphisms.
    Nucleic Acids Res. 2000 Jan 1;28(1):352-5 PMID: 10592272
  2. The cancer genome anatomy project: building an annotated gene index.
    Trends Genet. 2000 Mar;16(3):103-6 PMID: 10689348
  3. GeneLynx: a gene-centric portal to the human genome.
    Genome Res. 2001 Dec;11(12):2151-7 PMID: 11731507
  4. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders.
    Nucleic Acids Res. 2002 Jan 1;30(1):52-5 PMID: 11752252
  5. BLAT--the BLAST-like alignment tool.
    Genome Res. 2002 Apr;12(4):656-64 PMID: 11932250
  6. The human genome browser at UCSC.
    Genome Res. 2002 Jun;12(6):996-1006 PMID: 12045153
  7. Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE.
    Nucleic Acids Res. 2003 Jan 1;31(1):142-6 PMID: 12519968
  8. SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data.
    Nucleic Acids Res. 2003 Jan 1;31(1):219-23 PMID: 12519986
  9. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes.
    Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9 PMID: 14500911
  10. The UCSC Table Browser data retrieval tool.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6 PMID: 14681465
  11. The International HapMap Project.
    Nature. 2003 Dec 18;426(6968):789-96 PMID: 14685227
  12. Aligning multiple genomic sequences with the threaded blockset aligner.
    Genome Res. 2004 Apr;14(4):708-15 PMID: 15060014
  13. Gene expression nervous system atlas (GENSAT).
    Nat Neurosci. 2004 May;7(5):483 PMID: 15114362
  14. Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
    PLoS Biol. 2004 Jun;2(6):e162 PMID: 15103394
  15. Large-scale copy number polymorphism in the human genome.
    Science. 2004 Jul 23;305(5683):525-8 PMID: 15273396
  16. 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
  17. The ENCODE (ENCyclopedia Of DNA Elements) Project.
    Science. 2004 Oct 22;306(5696):636-40 PMID: 15499007
  18. The UCSC Proteome Browser.
    Nucleic Acids Res. 2005 Jan 1;33(Database issue):D454-8 PMID: 15608236
  19. Whole-genome patterns of common DNA variation in three human populations.
    Science. 2005 Feb 18;307(5712):1072-9 PMID: 15718463
  20. Exploring relationships and mining data with the UCSC Gene Sorter.
    Genome Res. 2005 May;15(5):737-41 PMID: 15867434
  21. Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences.
    Genome Res. 2005 Aug;15(8):1051-60 PMID: 16024817
  22. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
    Genome Res. 2005 Aug;15(8):1034-50 PMID: 16024819
  23. Computational screening of conserved genomic DNA in search of functional noncoding elements.
    Nat Methods. 2005 Jul;2(7):535-45 PMID: 16170870
  24. GenBank.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D16-20 PMID: 16381837
  25. The Universal Protein Resource (UniProt): an expanding universe of protein information.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D187-91 PMID: 16381842
  26. The HUGO Gene Nomenclature Database, 2006 updates.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D319-21 PMID: 16381876
  27. The Gene Ontology (GO) project in 2006.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D322-6 PMID: 16381878
  28. From genomics to chemical genomics: new developments in KEGG.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D354-7 PMID: 16381885
  29. Human protein reference database--2006 update.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D411-4 PMID: 16381900
  30. Ensembl 2006.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D556-61 PMID: 16381931
  31. The Mouse Genome Database (MGD): updates and enhancements.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D562-7 PMID: 16381933
  32. The UCSC Genome Browser Database: update 2006.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D590-8 PMID: 16381938
  33. The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D642-8 PMID: 16381950
  34. Towards the integration of spatially and temporally resolved murine gene expression databases.
    Trends Genet. 2006 Apr;22(4):211-7 PMID: 16499990
  35. The UCSC Known Genes.
    Bioinformatics. 2006 May 1;22(9):1036-46 PMID: 16500937
  36. An RNA gene expressed during cortical development evolved rapidly in humans.
    Nature. 2006 Sep 14;443(7108):167-72 PMID: 16915236
  37. Variation resources at UC Santa Cruz.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D716-20 PMID: 17151077
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkl928
Email
kuhn@soe.ucsc.edu
Published
2007-01-00
Epub
2006-00-16
Pages
D668-73
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1669757
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkl928 PMC Full Text View journal details
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