The UCSC Genome Browser database: Extensions and updates 2013

Laurence R. Meyer, Ann S. Zweig, Angie S. Hinrichs, Donna Karolchik, Robert M. Kuhn, Matthew Wong, Cricket A. Sloan, Kate R. Rosenbloom, Greg Roe, Brooke Rhead, Brian J. Raney, Andy Pohl, Venkat S. Malladi, Chin H. Li, Brian T. Lee, Katrina Learned, Vanessa Kirkup, Fan Hsu, Steve Heitner, Rachel A. HarteMaximilian Haeussler, Luvina Guruvadoo, Mary Goldman, Belinda M. Giardine, Pauline A. Fujita, Timothy R. Dreszer, Mark Diekhans, Melissa S. Cline, Hiram Clawson, Galt P. Barber, David Haussler, W. James Kent

Research output: Contribution to journalArticle

540 Citations (Scopus)

Abstract

The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic datasets. As of September 2012, genomic sequence and a basic set of annotation 'tracks' are provided for 63 organisms, including 26 mammals, 13 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms, yeast and sea hare. In the past year 19 new genome assemblies have been added, and we anticipate releasing another 28 in early 2013. Further, a large number of annotation tracks have been either added, updated by contributors or remapped to the latest human reference genome. Among these are an updated UCSC Genes track for human and mouse assemblies. We have also introduced several features to improve usability, including new navigation menus. This article provides an update to the UCSC Genome Browser database, which has been previously featured in the Database issue of this journal.

Original languageEnglish (US)
Pages (from-to)D64-D69
JournalNucleic acids research
Volume41
Issue numberD1
DOIs
StatePublished - Jan 1 2013
Externally publishedYes

Fingerprint

Genome
Databases
Hares
Human Genome
Invertebrates
Oceans and Seas
Insects
Vertebrates
Mammals
Yeasts
Genes
Datasets

ASJC Scopus subject areas

  • Genetics

Cite this

Meyer, L. R., Zweig, A. S., Hinrichs, A. S., Karolchik, D., Kuhn, R. M., Wong, M., ... Kent, W. J. (2013). The UCSC Genome Browser database: Extensions and updates 2013. Nucleic acids research, 41(D1), D64-D69. https://doi.org/10.1093/nar/gks1048

The UCSC Genome Browser database : Extensions and updates 2013. / Meyer, Laurence R.; Zweig, Ann S.; Hinrichs, Angie S.; Karolchik, Donna; Kuhn, Robert M.; Wong, Matthew; Sloan, Cricket A.; Rosenbloom, Kate R.; Roe, Greg; Rhead, Brooke; Raney, Brian J.; Pohl, Andy; Malladi, Venkat S.; Li, Chin H.; Lee, Brian T.; Learned, Katrina; Kirkup, Vanessa; Hsu, Fan; Heitner, Steve; Harte, Rachel A.; Haeussler, Maximilian; Guruvadoo, Luvina; Goldman, Mary; Giardine, Belinda M.; Fujita, Pauline A.; Dreszer, Timothy R.; Diekhans, Mark; Cline, Melissa S.; Clawson, Hiram; Barber, Galt P.; Haussler, David; Kent, W. James.

In: Nucleic acids research, Vol. 41, No. D1, 01.01.2013, p. D64-D69.

Research output: Contribution to journalArticle

Meyer, LR, Zweig, AS, Hinrichs, AS, Karolchik, D, Kuhn, RM, Wong, M, Sloan, CA, Rosenbloom, KR, Roe, G, Rhead, B, Raney, BJ, Pohl, A, Malladi, VS, Li, CH, Lee, BT, Learned, K, Kirkup, V, Hsu, F, Heitner, S, Harte, RA, Haeussler, M, Guruvadoo, L, Goldman, M, Giardine, BM, Fujita, PA, Dreszer, TR, Diekhans, M, Cline, MS, Clawson, H, Barber, GP, Haussler, D & Kent, WJ 2013, 'The UCSC Genome Browser database: Extensions and updates 2013', Nucleic acids research, vol. 41, no. D1, pp. D64-D69. https://doi.org/10.1093/nar/gks1048
Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M et al. The UCSC Genome Browser database: Extensions and updates 2013. Nucleic acids research. 2013 Jan 1;41(D1):D64-D69. https://doi.org/10.1093/nar/gks1048
Meyer, Laurence R. ; Zweig, Ann S. ; Hinrichs, Angie S. ; Karolchik, Donna ; Kuhn, Robert M. ; Wong, Matthew ; Sloan, Cricket A. ; Rosenbloom, Kate R. ; Roe, Greg ; Rhead, Brooke ; Raney, Brian J. ; Pohl, Andy ; Malladi, Venkat S. ; Li, Chin H. ; Lee, Brian T. ; Learned, Katrina ; Kirkup, Vanessa ; Hsu, Fan ; Heitner, Steve ; Harte, Rachel A. ; Haeussler, Maximilian ; Guruvadoo, Luvina ; Goldman, Mary ; Giardine, Belinda M. ; Fujita, Pauline A. ; Dreszer, Timothy R. ; Diekhans, Mark ; Cline, Melissa S. ; Clawson, Hiram ; Barber, Galt P. ; Haussler, David ; Kent, W. James. / The UCSC Genome Browser database : Extensions and updates 2013. In: Nucleic acids research. 2013 ; Vol. 41, No. D1. pp. D64-D69.
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