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The UCSC Genome Browser Database: update 2009.

The UCSC Genome Browser Database (GBD, is a publicly available collection of genome assembly sequence data and integrated annotations for a large number of organisms, including extensive comparative-genomic resources. In the past year, 13 new genome assemblies have been added, including two important primate species, orangutan and marmoset, bringing the total to 46 assemblies for 24 different vertebrates and 39 assemblies for 22 different invertebrate animals. The GBD datasets may be viewed graphically with the UCSC Genome Browser, which uses a coordinate-based display system allowing users to juxtapose a wide variety of data. These data include all mRNAs from GenBank mapped to all organisms, RefSeq alignments, gene predictions, regulatory elements, gene expression data, repeats, SNPs and other variation data, as well as pairwise and multiple-genome alignments. A variety of other bioinformatics tools are also provided, including BLAT, the Table Browser, the Gene Sorter, the Proteome Browser, VisiGene and Genome Graphs.

Pubmed ID: 18996895


  • Kuhn RM
  • Karolchik D
  • Zweig AS
  • Wang T
  • Smith KE
  • Rosenbloom KR
  • Rhead B
  • Raney BJ
  • Pohl A
  • Pheasant M
  • Meyer L
  • Hsu F
  • Hinrichs AS
  • Harte RA
  • Giardine B
  • Fujita P
  • Diekhans M
  • Dreszer T
  • Clawson H
  • Barber GP
  • Haussler D
  • Kent WJ


Nucleic acids research

Publication Data

January 16, 2009

Associated Grants

  • Agency: NHGRI NIH HHS, Id: 1P41HG002371-08
  • Agency: NHGRI NIH HHS, Id: 1P41HG004568-01
  • Agency: NHGRI NIH HHS, Id: 1U54HG004555-01
  • Agency: NHGRI NIH HHS, Id: 2P41HG002371-08
  • Agency: NHGRI NIH HHS, Id: 2U41 HG004269-02
  • Agency: NCI NIH HHS, Id: N01-CO-12400
  • Agency: NHGRI NIH HHS, Id: U54 HG004555
  • Agency: NHGRI NIH HHS, Id: U54 HG004555-02
  • Agency: Howard Hughes Medical Institute, Id:

Mesh Terms

  • Animals
  • Chromosome Mapping
  • Computer Graphics
  • Databases, Nucleic Acid
  • Gene Expression
  • Genetic Variation
  • Genomics
  • Humans
  • RNA, Messenger
  • Software
  • User-Computer Interface