The UCSC genome browser database: Update 2010

Brooke Rhead, Donna Karolchik, Robert M. Kuhn, Angie S. Hinrichs, Ann S. Zweig, Pauline A. Fujita, Mark Diekhans, Kayla E. Smith, Kate R. Rosenbloom, Brian J. Raney, Andy Pohl, Michael Pheasant, Laurence R. Meyer, Katrina Learned, Fan Hsu, Jennifer Hillman-Jackson, Rachel A. Harte, Belinda Giardine, Timothy R. Dreszer, Hiram ClawsonGalt P. Barber, David Haussler, W. James Kent

Research output: Contribution to journalArticle

477 Citations (Scopus)

Abstract

The University of California, Santa Cruz (UCSC) Genome Browser website (http://genome.ucsc.edu/) provides a large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users' own annotation data. As of September 2009, genomic sequence and a basic set of annotation 'tracks' are provided for 47 organisms, including 14 mammals, 10 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms and a yeast. New data highlights this year include an updated human genome browser, a 44-species multiple sequence alignment track, improved variation and phenotype tracks and 16 new genome-wide ENCODE tracks. New features include drag-and-zoom navigation, a Wiki track for user-added annotations, new custom track formats for large datasets (bigBed and bigWig), a new multiple alignment output tool, links to variation and protein structure tools, in silico PCR utility enhancements, and improved track configuration tools.

Original languageEnglish (US)
Article numbergkp939
Pages (from-to)D613-D619
JournalNucleic acids research
Volume38
Issue numberSUPPL.1
DOIs
StatePublished - Nov 10 2009

Fingerprint

Genome
Databases
Sequence Alignment
Human Genome
Invertebrates
Computer Simulation
Insects
Vertebrates
Mammals
Yeasts
Phenotype
Polymerase Chain Reaction
Proteins
Data Curation
Datasets

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Rhead, B., Karolchik, D., Kuhn, R. M., Hinrichs, A. S., Zweig, A. S., Fujita, P. A., ... Kent, W. J. (2009). The UCSC genome browser database: Update 2010. Nucleic acids research, 38(SUPPL.1), D613-D619. [gkp939]. https://doi.org/10.1093/nar/gkp939
Rhead, Brooke ; Karolchik, Donna ; Kuhn, Robert M. ; Hinrichs, Angie S. ; Zweig, Ann S. ; Fujita, Pauline A. ; Diekhans, Mark ; Smith, Kayla E. ; Rosenbloom, Kate R. ; Raney, Brian J. ; Pohl, Andy ; Pheasant, Michael ; Meyer, Laurence R. ; Learned, Katrina ; Hsu, Fan ; Hillman-Jackson, Jennifer ; Harte, Rachel A. ; Giardine, Belinda ; Dreszer, Timothy R. ; Clawson, Hiram ; Barber, Galt P. ; Haussler, David ; Kent, W. James. / The UCSC genome browser database : Update 2010. In: Nucleic acids research. 2009 ; Vol. 38, No. SUPPL.1. pp. D613-D619.
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abstract = "The University of California, Santa Cruz (UCSC) Genome Browser website (http://genome.ucsc.edu/) provides a large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users' own annotation data. As of September 2009, genomic sequence and a basic set of annotation 'tracks' are provided for 47 organisms, including 14 mammals, 10 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms and a yeast. New data highlights this year include an updated human genome browser, a 44-species multiple sequence alignment track, improved variation and phenotype tracks and 16 new genome-wide ENCODE tracks. New features include drag-and-zoom navigation, a Wiki track for user-added annotations, new custom track formats for large datasets (bigBed and bigWig), a new multiple alignment output tool, links to variation and protein structure tools, in silico PCR utility enhancements, and improved track configuration tools.",
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Rhead, B, Karolchik, D, Kuhn, RM, Hinrichs, AS, Zweig, AS, Fujita, PA, Diekhans, M, Smith, KE, Rosenbloom, KR, Raney, BJ, Pohl, A, Pheasant, M, Meyer, LR, Learned, K, Hsu, F, Hillman-Jackson, J, Harte, RA, Giardine, B, Dreszer, TR, Clawson, H, Barber, GP, Haussler, D & Kent, WJ 2009, 'The UCSC genome browser database: Update 2010', Nucleic acids research, vol. 38, no. SUPPL.1, gkp939, pp. D613-D619. https://doi.org/10.1093/nar/gkp939

The UCSC genome browser database : Update 2010. / Rhead, Brooke; Karolchik, Donna; Kuhn, Robert M.; Hinrichs, Angie S.; Zweig, Ann S.; Fujita, Pauline A.; Diekhans, Mark; Smith, Kayla E.; Rosenbloom, Kate R.; Raney, Brian J.; Pohl, Andy; Pheasant, Michael; Meyer, Laurence R.; Learned, Katrina; Hsu, Fan; Hillman-Jackson, Jennifer; Harte, Rachel A.; Giardine, Belinda; Dreszer, Timothy R.; Clawson, Hiram; Barber, Galt P.; Haussler, David; Kent, W. James.

In: Nucleic acids research, Vol. 38, No. SUPPL.1, gkp939, 10.11.2009, p. D613-D619.

Research output: Contribution to journalArticle

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AU - Rhead, Brooke

AU - Karolchik, Donna

AU - Kuhn, Robert M.

AU - Hinrichs, Angie S.

AU - Zweig, Ann S.

AU - Fujita, Pauline A.

AU - Diekhans, Mark

AU - Smith, Kayla E.

AU - Rosenbloom, Kate R.

AU - Raney, Brian J.

AU - Pohl, Andy

AU - Pheasant, Michael

AU - Meyer, Laurence R.

AU - Learned, Katrina

AU - Hsu, Fan

AU - Hillman-Jackson, Jennifer

AU - Harte, Rachel A.

AU - Giardine, Belinda

AU - Dreszer, Timothy R.

AU - Clawson, Hiram

AU - Barber, Galt P.

AU - Haussler, David

AU - Kent, W. James

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Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA et al. The UCSC genome browser database: Update 2010. Nucleic acids research. 2009 Nov 10;38(SUPPL.1):D613-D619. gkp939. https://doi.org/10.1093/nar/gkp939