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. Li; Laurence R. Meyer; Andy Pohl; Brian J. Raney; Kate R. Rosenbloom; Kayla E. Smith; David Haussler; W. James Kent

doi:10.1093/nar/gkq963

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

Biochemistry & Molecular Biology

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846 Scopus citations

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 language	English (US)
Pages (from-to)	D876-D882
Journal	Nucleic acids research
Volume	39
Issue number	SUPPL. 1
DOIs	https://doi.org/10.1093/nar/gkq963
State	Published - Jan 2011

All Science Journal Classification (ASJC) codes

Genetics

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10.1093/nar/gkq963

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Fujita, P. A., Rhead, B., Zweig, A. S., Hinrichs, A. S., Karolchik, D., Cline, M. S., Goldman, M., Barber, G. P., Clawson, H., Coelho, A., Diekhans, M., Dreszer, T. R., Giardine, B. M., Harte, R. A., Hillman-Jackson, J., Hsu, F., Kirkup, V., Kuhn, R. M., Learned, K., ... 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

@article{e0b53d76c9df494294b9f3ee7875452d,

title = "The UCSC genome browser database: Update 2011",

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.",

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

note = "Funding Information: Grants from the NHGRI (P41HG002371 to G.B., H.C., M.D., P.F., A.H., F.H., D.K., V.K., W.J.K., R.K., C.L., L.M, B.R. and A.Z.; U41HG004568 to M.C., T.D., M.G., F.H., W.J.K., K.L., K.R. and B.R.); NCI (U24CA143858 to F.H. and W.J.K); subcontracts from the NIDCR (U01DE20057 to G.B. and R.K.), NHGRI (P01HG5062 to G.B., W.J.K. and B.R; U54HG004555 to M.D. and R.H.; U41HG004269 to A.H. and W.J.K.; U01HG004695 to W.J.K.); NICHD (RC2HD064525 to H.C., A.H. and R.K.); NIEHS (U01ES017154 to W.J.K). Support from HHMI to D.H. Funding for open access charges: HHMI.",

year = "2011",

month = jan,

doi = "10.1093/nar/gkq963",

language = "English (US)",

volume = "39",

pages = "D876--D882",

journal = "Nucleic acids research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "SUPPL. 1",

}

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

TY - JOUR

T1 - The UCSC genome browser database

T2 - Update 2011

AU - Fujita, Pauline A.

AU - Rhead, Brooke

AU - Zweig, Ann S.

AU - Hinrichs, Angie S.

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.

AU - Giardine, Belinda M.

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.

AU - Haussler, David

AU - Kent, W. James

N1 - Funding Information: Grants from the NHGRI (P41HG002371 to G.B., H.C., M.D., P.F., A.H., F.H., D.K., V.K., W.J.K., R.K., C.L., L.M, B.R. and A.Z.; U41HG004568 to M.C., T.D., M.G., F.H., W.J.K., K.L., K.R. and B.R.); NCI (U24CA143858 to F.H. and W.J.K); subcontracts from the NIDCR (U01DE20057 to G.B. and R.K.), NHGRI (P01HG5062 to G.B., W.J.K. and B.R; U54HG004555 to M.D. and R.H.; U41HG004269 to A.H. and W.J.K.; U01HG004695 to W.J.K.); NICHD (RC2HD064525 to H.C., A.H. and R.K.); NIEHS (U01ES017154 to W.J.K). Support from HHMI to D.H. Funding for open access charges: HHMI.

PY - 2011/1

Y1 - 2011/1

N2 - 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.

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JF - Nucleic acids research

IS - SUPPL. 1

ER -

The UCSC genome browser database: Update 2011

Abstract

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