The UCSC Genome Browser Database: update 2006.

A. S. Hinrichs, D. Karolchik, R. Baertsch, G. P. Barber, G. Bejerano, H. Clawson, M. Diekhans, T. S. Furey, R. A. Harte, F. Hsu, Jennifer Lynne Jackson, R. M. Kuhn, J. S. Pedersen, A. Pohl, B. J. Raney, K. R. Rosenbloom, A. Siepel, K. E. Smith, C. W. Sugnet, A. Sultan-QurraieD. J. Thomas, H. Trumbower, R. J. Weber, M. Weirauch, A. S. Zweig, D. Haussler, W. J. Kent

Research output: Contribution to journalArticle

478 Citations (Scopus)

Abstract

The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, mRNA and expressed sequence tag evidence, comparative genomics, regulation, expression and variation data. The database is optimized to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. The Genome Browser displays a wide variety of annotations at all scales from single nucleotide level up to a full chromosome. The Table Browser provides direct access to the database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. The Gene Sorter allows filtering and comparison of genes by several metrics including expression data and several gene properties. BLAT and In Silico PCR search for sequences in entire genomes in seconds. These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD, browsing tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.

Original languageEnglish (US)
JournalNucleic acids research
Volume34
Issue numberDatabase issue
StatePublished - Jan 1 2006

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Genome
Databases
Genes
Data Mining
Information Storage and Retrieval
Expressed Sequence Tags
Proteome
Genomics
Documentation
Computer Simulation
Vertebrates
Nucleotides
Chromosomes
Polymerase Chain Reaction
Messenger RNA
Proteins

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Hinrichs, A. S., Karolchik, D., Baertsch, R., Barber, G. P., Bejerano, G., Clawson, H., ... Kent, W. J. (2006). The UCSC Genome Browser Database: update 2006. Nucleic acids research, 34(Database issue).
Hinrichs, A. S. ; Karolchik, D. ; Baertsch, R. ; Barber, G. P. ; Bejerano, G. ; Clawson, H. ; Diekhans, M. ; Furey, T. S. ; Harte, R. A. ; Hsu, F. ; Jackson, Jennifer Lynne ; Kuhn, R. M. ; Pedersen, J. S. ; Pohl, A. ; Raney, B. J. ; Rosenbloom, K. R. ; Siepel, A. ; Smith, K. E. ; Sugnet, C. W. ; Sultan-Qurraie, A. ; Thomas, D. J. ; Trumbower, H. ; Weber, R. J. ; Weirauch, M. ; Zweig, A. S. ; Haussler, D. ; Kent, W. J. / The UCSC Genome Browser Database : update 2006. In: Nucleic acids research. 2006 ; Vol. 34, No. Database issue.
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Hinrichs, AS, Karolchik, D, Baertsch, R, Barber, GP, Bejerano, G, Clawson, H, Diekhans, M, Furey, TS, Harte, RA, Hsu, F, Jackson, JL, Kuhn, RM, Pedersen, JS, Pohl, A, Raney, BJ, Rosenbloom, KR, Siepel, A, Smith, KE, Sugnet, CW, Sultan-Qurraie, A, Thomas, DJ, Trumbower, H, Weber, RJ, Weirauch, M, Zweig, AS, Haussler, D & Kent, WJ 2006, 'The UCSC Genome Browser Database: update 2006.', Nucleic acids research, vol. 34, no. Database issue.

The UCSC Genome Browser Database : update 2006. / Hinrichs, A. S.; Karolchik, D.; Baertsch, R.; Barber, G. P.; Bejerano, G.; Clawson, H.; Diekhans, M.; Furey, T. S.; Harte, R. A.; Hsu, F.; Jackson, Jennifer Lynne; Kuhn, R. M.; Pedersen, J. S.; Pohl, A.; Raney, B. J.; Rosenbloom, K. R.; Siepel, A.; Smith, K. E.; Sugnet, C. W.; Sultan-Qurraie, A.; Thomas, D. J.; Trumbower, H.; Weber, R. J.; Weirauch, M.; Zweig, A. S.; Haussler, D.; Kent, W. J.

In: Nucleic acids research, Vol. 34, No. Database issue, 01.01.2006.

Research output: Contribution to journalArticle

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T1 - The UCSC Genome Browser Database

T2 - update 2006.

AU - Hinrichs, A. S.

AU - Karolchik, D.

AU - Baertsch, R.

AU - Barber, G. P.

AU - Bejerano, G.

AU - Clawson, H.

AU - Diekhans, M.

AU - Furey, T. S.

AU - Harte, R. A.

AU - Hsu, F.

AU - Jackson, Jennifer Lynne

AU - Kuhn, R. M.

AU - Pedersen, J. S.

AU - Pohl, A.

AU - Raney, B. J.

AU - Rosenbloom, K. R.

AU - Siepel, A.

AU - Smith, K. E.

AU - Sugnet, C. W.

AU - Sultan-Qurraie, A.

AU - Thomas, D. J.

AU - Trumbower, H.

AU - Weber, R. J.

AU - Weirauch, M.

AU - Zweig, A. S.

AU - Haussler, D.

AU - Kent, W. J.

PY - 2006/1/1

Y1 - 2006/1/1

N2 - The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, mRNA and expressed sequence tag evidence, comparative genomics, regulation, expression and variation data. The database is optimized to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. The Genome Browser displays a wide variety of annotations at all scales from single nucleotide level up to a full chromosome. The Table Browser provides direct access to the database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. The Gene Sorter allows filtering and comparison of genes by several metrics including expression data and several gene properties. BLAT and In Silico PCR search for sequences in entire genomes in seconds. These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD, browsing tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.

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Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H et al. The UCSC Genome Browser Database: update 2006. Nucleic acids research. 2006 Jan 1;34(Database issue).