The UCSC Genome Browser Database: 2008 update.

D Karolchik; R M Kuhn; R Baertsch; G P Barber; H Clawson; M Diekhans; B Giardine; R A Harte; A S Hinrichs; F Hsu; K M Kober; W Miller; Jakob Skou Pedersen; A Pohl; B J Raney; B Rhead; K R Rosenbloom; K E Smith; M Stanke; A Thakkapallayil; H Trumbower; T Wang; A S Zweig; D Haussler; W J Kent

doi:10.1093/nar/gkm966

The UCSC Genome Browser Database: 2008 update.

D Karolchik, R M Kuhn, R Baertsch, G P Barber, H Clawson, M Diekhans, B Giardine, R A Harte, A S Hinrichs, F Hsu, K M Kober, W Miller, Jakob Skou Pedersen, A Pohl, B J Raney, B Rhead, K R Rosenbloom, K E Smith, M Stanke, A ThakkapallayilH Trumbower, T Wang, A S Zweig, D Haussler, W J Kent

Functional Genomics

410 Citations (Scopus)

Abstract

The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrate and 21 invertebrate species as of September 2007. For each assembly, the GBD contains a collection of annotation data aligned to the genomic sequence. Highlights of this year's additions include a 28-species human-based vertebrate conservation annotation, an enhanced UCSC Genes set, and more human variation, MGC, and ENCODE data. The database is optimized for fast interactive performance with a set of web-based tools that may be used to view, manipulate, filter and download the annotation data. New toolset features include the Genome Graphs tool for displaying genome-wide data sets, session saving and sharing, better custom track management, expanded Genome Browser configuration options and a Genome Browser wiki site. The downloadable GBD data, the companion Genome Browser toolset and links to documentation and related information can be found at: http://genome.ucsc.edu/.

Original language	English
Journal	Nucleic Acids Research
Volume	36
Issue number	Database issue
Pages (from-to)	D773-9
ISSN	0305-1048
DOIs	https://doi.org/10.1093/nar/gkm966
Publication status	Published - 2007

Keywords

Faculty of Science
Animals
Computer Graphics
Databases
Nucleic Acid
Genomics
Humans
Internet
Invertebrates
Sequence Alignment
User-Computer Interface
Variation (Genetics)
Vertebrates

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Karolchik, D., Kuhn, R. M., Baertsch, R., Barber, G. P., Clawson, H., Diekhans, M., Giardine, B., Harte, R. A., Hinrichs, A. S., Hsu, F., Kober, K. M., Miller, W., Pedersen, J. S., Pohl, A., Raney, B. J., Rhead, B., Rosenbloom, K. R., Smith, K. E., Stanke, M., ... Kent, W. J. (2007). The UCSC Genome Browser Database: 2008 update. Nucleic Acids Research, 36(Database issue), D773-9. https://doi.org/10.1093/nar/gkm966

Karolchik, D, Kuhn, RM, Baertsch, R, Barber, GP, Clawson, H, Diekhans, M, Giardine, B, Harte, RA, Hinrichs, AS, Hsu, F, Kober, KM, Miller, W, Pedersen, JS, Pohl, A, Raney, BJ, Rhead, B, Rosenbloom, KR, Smith, KE, Stanke, M, Thakkapallayil, A, Trumbower, H, Wang, T, Zweig, AS, Haussler, D & Kent, WJ 2007, 'The UCSC Genome Browser Database: 2008 update.', Nucleic Acids Research, vol. 36, no. Database issue, pp. D773-9. https://doi.org/10.1093/nar/gkm966

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abstract = "The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrate and 21 invertebrate species as of September 2007. For each assembly, the GBD contains a collection of annotation data aligned to the genomic sequence. Highlights of this year's additions include a 28-species human-based vertebrate conservation annotation, an enhanced UCSC Genes set, and more human variation, MGC, and ENCODE data. The database is optimized for fast interactive performance with a set of web-based tools that may be used to view, manipulate, filter and download the annotation data. New toolset features include the Genome Graphs tool for displaying genome-wide data sets, session saving and sharing, better custom track management, expanded Genome Browser configuration options and a Genome Browser wiki site. The downloadable GBD data, the companion Genome Browser toolset and links to documentation and related information can be found at: http://genome.ucsc.edu/.",

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AU - Diekhans, M

AU - Giardine, B

AU - Harte, R A

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AU - Kober, K M

AU - Miller, W

AU - Pedersen, Jakob Skou

AU - Pohl, A

AU - Raney, B J

AU - Rhead, B

AU - Rosenbloom, K R

AU - Smith, K E

AU - Stanke, M

AU - Thakkapallayil, A

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AU - Zweig, A S

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AU - Kent, W J

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AB - The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrate and 21 invertebrate species as of September 2007. For each assembly, the GBD contains a collection of annotation data aligned to the genomic sequence. Highlights of this year's additions include a 28-species human-based vertebrate conservation annotation, an enhanced UCSC Genes set, and more human variation, MGC, and ENCODE data. The database is optimized for fast interactive performance with a set of web-based tools that may be used to view, manipulate, filter and download the annotation data. New toolset features include the Genome Graphs tool for displaying genome-wide data sets, session saving and sharing, better custom track management, expanded Genome Browser configuration options and a Genome Browser wiki site. The downloadable GBD data, the companion Genome Browser toolset and links to documentation and related information can be found at: http://genome.ucsc.edu/.

KW - Faculty of Science

KW - Animals

KW - Computer Graphics

KW - Databases

KW - Nucleic Acid

KW - Genomics

KW - Humans

KW - Internet

KW - Invertebrates

KW - Sequence Alignment

KW - User-Computer Interface

KW - Variation (Genetics)

KW - Vertebrates

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JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - Database issue

ER -

The UCSC Genome Browser Database: 2008 update.

Abstract

Keywords

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