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; J Hillman-Jackson; R M Kuhn; Jakob Skou Pedersen; A Pohl; B J Raney; K R Rosenbloom; A Siepel; K E Smith; C W Sugnet; A Sultan-Qurraie; D J Thomas; H Trumbower; R J Weber; M Weirauch; A S Zweig; D Haussler; W J Kent

doi:10.1093/nar/gkj144

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, J Hillman-Jackson, R M Kuhn, Jakob Skou 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

Functional Genomics

584 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 language	English
Journal	Nucleic Acids Research
Volume	34
Issue number	Database issue
Pages (from-to)	D590-8
ISSN	0305-1048
DOIs	https://doi.org/10.1093/nar/gkj144
Publication status	Published - 2006

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Hinrichs, A. S., Karolchik, D., Baertsch, R., Barber, G. P., Bejerano, G., Clawson, H., Diekhans, M., Furey, T. S., Harte, R. A., Hsu, F., Hillman-Jackson, J., Kuhn, R. M., Pedersen, J. S., Pohl, A., Raney, B. J., Rosenbloom, K. R., Siepel, A., Smith, K. E., Sugnet, C. W., ... Kent, W. J. (2006). The UCSC Genome Browser Database: update 2006. Nucleic Acids Research, 34(Database issue), D590-8. https://doi.org/10.1093/nar/gkj144

Hinrichs, AS, Karolchik, D, Baertsch, R, Barber, GP, Bejerano, G, Clawson, H, Diekhans, M, Furey, TS, Harte, RA, Hsu, F, Hillman-Jackson, J, 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, pp. D590-8. https://doi.org/10.1093/nar/gkj144

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title = "The UCSC Genome Browser Database: update 2006.",

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/.",

author = "Hinrichs, {A S} and D Karolchik and R Baertsch and Barber, {G P} and G Bejerano and H Clawson and M Diekhans and Furey, {T S} and Harte, {R A} and F Hsu and J Hillman-Jackson and Kuhn, {R M} and Pedersen, {Jakob Skou} and A Pohl and Raney, {B J} and Rosenbloom, {K R} and A Siepel and Smith, {K E} and Sugnet, {C W} and A Sultan-Qurraie and Thomas, {D J} and H Trumbower and Weber, {R J} and M Weirauch and Zweig, {A S} and D Haussler and Kent, {W J}",

note = "Keywords: Amino Acid Sequence; Animals; California; Computer Graphics; Databases, Genetic; Dogs; Gene Expression; Genes; Genomics; Humans; Internet; Mice; Polymorphism, Single Nucleotide; Proteins; Proteomics; Rats; Sequence Alignment; Software; User-Computer Interface",

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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 - Hillman-Jackson, J

AU - Kuhn, R M

AU - Pedersen, Jakob Skou

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

N1 - Keywords: Amino Acid Sequence; Animals; California; Computer Graphics; Databases, Genetic; Dogs; Gene Expression; Genes; Genomics; Humans; Internet; Mice; Polymorphism, Single Nucleotide; Proteins; Proteomics; Rats; Sequence Alignment; Software; User-Computer Interface

PY - 2006

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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/.

AB - 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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DO - 10.1093/nar/gkj144

M3 - Journal article

C2 - 16381938

SN - 0305-1048

VL - 34

SP - D590-8

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - Database issue

ER -

The UCSC Genome Browser Database: update 2006.

Abstract

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