The UCSC genome browser database: Update 2011

Pauline A. Fujita, Brooke Rhead, Ann S. Zweig, Angie S. Hinrichs, Donna Karolchik, Melissa S. Cline, Mary Goldman, Galt P. Barber, Hiram Clawson, Antonio Coelho, Mark Diekhans, Timothy R. Dreszer, Belinda M. Giardine, Rachel A. Harte, Jennifer Hillman-Jackson, Fan Hsu, Vanessa Kirkup, Robert M. Kuhn, Katrina Learned, Chin H. LiLaurence R. Meyer, Andy Pohl, Brian J. Raney, Kate R. Rosenbloom, Kayla E. Smith, David Haussler, W. James Kent

Research output: Contribution to journalArticle

793 Citations (Scopus)

Abstract

The University of California, Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online access to a database of genomic sequence and annotation data for a wide variety of organisms. The Browser also has many tools for visualizing, comparing and analyzing both publicly available and user-generated genomic data sets, aligning sequences and uploading user data. Among the features released this year are a gene search tool and annotation track drag-reorder functionality as well as support for BAM and BigWig/BigBed file formats. New display enhancements include overlay of multiple wiggle tracks through use of transparent coloring, options for displaying transformed wiggle data, a 'mean+whiskers' windowing function for display of wiggle data at high zoom levels, and more color schemes for microarray data. New data highlights include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA editing track, and a zebrafish Conservation track. We also describe updates to existing tracks.

Original languageEnglish (US)
Pages (from-to)D876-D882
JournalNucleic acids research
Volume39
Issue numberSUPPL. 1
DOIs
StatePublished - Jan 1 2011

Fingerprint

Genome
Databases
Neanderthals
RNA Editing
Data Display
Vibrissae
Zebrafish
Color
Phenotype
Genes
Data Curation
Datasets

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Fujita, P. A., Rhead, B., Zweig, A. S., Hinrichs, A. S., Karolchik, D., Cline, M. S., ... Kent, W. J. (2011). The UCSC genome browser database: Update 2011. Nucleic acids research, 39(SUPPL. 1), D876-D882. https://doi.org/10.1093/nar/gkq963
Fujita, Pauline A. ; Rhead, Brooke ; Zweig, Ann S. ; Hinrichs, Angie S. ; Karolchik, Donna ; Cline, Melissa S. ; Goldman, Mary ; Barber, Galt P. ; Clawson, Hiram ; Coelho, Antonio ; Diekhans, Mark ; Dreszer, Timothy R. ; Giardine, Belinda M. ; Harte, Rachel A. ; Hillman-Jackson, Jennifer ; Hsu, Fan ; Kirkup, Vanessa ; Kuhn, Robert M. ; Learned, Katrina ; Li, Chin H. ; Meyer, Laurence R. ; Pohl, Andy ; Raney, Brian J. ; Rosenbloom, Kate R. ; Smith, Kayla E. ; Haussler, David ; Kent, W. James. / The UCSC genome browser database : Update 2011. In: Nucleic acids research. 2011 ; Vol. 39, No. SUPPL. 1. pp. D876-D882.
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Fujita, PA, Rhead, B, Zweig, AS, Hinrichs, AS, Karolchik, D, Cline, MS, Goldman, M, Barber, GP, Clawson, H, Coelho, A, Diekhans, M, Dreszer, TR, Giardine, BM, Harte, RA, Hillman-Jackson, J, Hsu, F, Kirkup, V, Kuhn, RM, Learned, K, Li, CH, Meyer, LR, Pohl, A, Raney, BJ, Rosenbloom, KR, Smith, KE, Haussler, D & Kent, WJ 2011, 'The UCSC genome browser database: Update 2011', Nucleic acids research, vol. 39, no. SUPPL. 1, pp. D876-D882. https://doi.org/10.1093/nar/gkq963

The UCSC genome browser database : Update 2011. / Fujita, Pauline A.; Rhead, Brooke; Zweig, Ann S.; Hinrichs, Angie S.; Karolchik, Donna; Cline, Melissa S.; Goldman, Mary; Barber, Galt P.; Clawson, Hiram; Coelho, Antonio; Diekhans, Mark; Dreszer, Timothy R.; Giardine, Belinda M.; Harte, Rachel A.; Hillman-Jackson, Jennifer; Hsu, Fan; Kirkup, Vanessa; Kuhn, Robert M.; Learned, Katrina; Li, Chin H.; Meyer, Laurence R.; Pohl, Andy; Raney, Brian J.; Rosenbloom, Kate R.; Smith, Kayla E.; Haussler, David; Kent, W. James.

In: Nucleic acids research, Vol. 39, No. SUPPL. 1, 01.01.2011, p. D876-D882.

Research output: Contribution to journalArticle

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AU - Karolchik, Donna

AU - Cline, Melissa S.

AU - Goldman, Mary

AU - Barber, Galt P.

AU - Clawson, Hiram

AU - Coelho, Antonio

AU - Diekhans, Mark

AU - Dreszer, Timothy R.

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AU - Harte, Rachel A.

AU - Hillman-Jackson, Jennifer

AU - Hsu, Fan

AU - Kirkup, Vanessa

AU - Kuhn, Robert M.

AU - Learned, Katrina

AU - Li, Chin H.

AU - Meyer, Laurence R.

AU - Pohl, Andy

AU - Raney, Brian J.

AU - Rosenbloom, Kate R.

AU - Smith, Kayla E.

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Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS et al. The UCSC genome browser database: Update 2011. Nucleic acids research. 2011 Jan 1;39(SUPPL. 1):D876-D882. https://doi.org/10.1093/nar/gkq963