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PMID: 18996895 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

The UCSC Genome Browser Database: update 2009.

Nucleic acids research ·Vol. 37 ·No. Database issue ·2009-01-00 ·Pages D755-61

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

Abstract

The UCSC Genome Browser Database (GBD, http://genome.ucsc.edu) 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.

MeSH Terms
Animals Chromosome Mapping Computer Graphics Databases, Nucleic Acid Gene Expression Genetic Variation Genomics Humans RNA, Messenger/chemistry Software User-Computer Interface
Chemicals
RNA, Messenger
Authors & Affiliations
22 authors, click to expand affiliations / ORCID
Kuhn R M
Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA. [email protected]
Karolchik D
Zweig A S
Wang T
Smith K E
Rosenbloom K R
Rhead B
Raney B J
Pohl A
Pheasant M
Meyer L
Hsu F
Hinrichs A S
Harte R A
Giardine B
Fujita P
Diekhans M
Dreszer T
Clawson H
Barber G P
Haussler D
Kent W J
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkn875
Email
[email protected]
Published
2009-01-00
Epub
2008-00-07
Pages
D755-61
Language
English
Region
England
NLM ID
0411011
PMCID
PMC2686463
Subset
IM
Grants
NHGRI NIH HHS · 1P41HG002371-08 · United States
NHGRI NIH HHS · 2U41 HG004269-02 · United States
NHGRI NIH HHS · 1U54HG004555-01 · United States
NHGRI NIH HHS · 2P41HG002371-08 · United States
Howard Hughes Medical Institute · United States
NHGRI NIH HHS · U54 HG004555-02 · United States
NHGRI NIH HHS · 1P41HG004568-01 · 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/gkn875 PMC Full Text View journal details
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