TY - JOUR
T1 - The UCSC Genome Browser Database
T2 - Update 2009
AU - Kuhn, R. M.
AU - Karolchik, D.
AU - Zweig, A. S.
AU - Wang, T.
AU - Smith, K. E.
AU - Rosenbloom, K. R.
AU - Rhead, B.
AU - Raney, B. J.
AU - Pohl, A.
AU - Pheasant, M.
AU - Meyer, L.
AU - Hsu, F.
AU - Hinrichs, A. S.
AU - Harte, R. A.
AU - Giardine, B.
AU - Fujita, P.
AU - Diekhans, M.
AU - Dreszer, T.
AU - Clawson, H.
AU - Barber, G. P.
AU - Haussler, D.
AU - Kent, W. J.
N1 - Funding Information:
The National Human Genome Research Institute (1P41HG002371-08 to UCSC Center for Genomic Science, 2P41HG002371-08 ENCODE supplement to UCSC Center for Genomic Science, 1P41HG004568-01 UCSC ENCODE Data Coordination Center, a subcontract on 2U41 HG004269-02 to L.Stein for A Data Coordination Center for modENCODE and a subcontract on 1U54HG004555-01 to T.Hubbard for Integrated Human Genome Annotation; Generation of a Reference Gene Set); National Cancer Institute (Contract No. N01-CO-12400 for Mammalian Gene Collection); the Howard Hughes Medical Institute (to D.H.). T.W. is a Helen Hay Whitney fellow. Funding for open access charge: the Howard Hughes Medical Institute.
PY - 2009
Y1 - 2009
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=58149178565&partnerID=8YFLogxK
U2 - 10.1093/nar/gkn875
DO - 10.1093/nar/gkn875
M3 - Article
C2 - 18996895
AN - SCOPUS:58149178565
SN - 0305-1048
VL - 37
SP - D755-D761
JO - Nucleic acids research
JF - Nucleic acids research
IS - SUPPL. 1
ER -