The UCSC genome browser database: update 2007.

R M Kuhn; D Karolchik; A S Zweig; H Trumbower; D J Thomas; A Thakkapallayil; C W Sugnet; M Stanke; K E Smith; A Siepel; K R Rosenbloom; B Rhead; B J Raney; A Pohl; Jakob Skou Pedersen; F Hsu; A S Hinrichs; R A Harte; M Diekhans; H Clawson; G Bejerano; G P Barber; R Baertsch; D Haussler; W J Kent

doi:10.1093/nar/gkl928

The UCSC genome browser database: update 2007.

R M Kuhn, D Karolchik, A S Zweig, H Trumbower, D J Thomas, A Thakkapallayil, C W Sugnet, M Stanke, K E Smith, A Siepel, K R Rosenbloom, B Rhead, B J Raney, A Pohl, Jakob Skou Pedersen, F Hsu, A S Hinrichs, R A Harte, M Diekhans, H ClawsonG Bejerano, G P Barber, R Baertsch, D Haussler, W J Kent

Functional Genomics

232 Citations (Scopus)

Abstract

The University of California, Santa Cruz Genome Browser Database contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up to a full chromosome and includes assembly data, genes and gene predictions, mRNA and EST alignments, and comparative genomics, regulation, expression and variation data. The database is optimized for fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. In the past year, 22 new assemblies and several new sets of human variation annotation have been released. New features include VisiGene, a fully integrated in situ hybridization image browser; phyloGif, for drawing evolutionary tree diagrams; a redesigned Custom Track feature; an expanded SNP annotation track; and many new display options. The Genome Browser, other 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	35
Issue number	Database issue
Pages (from-to)	D668-73
ISSN	0305-1048
DOIs	https://doi.org/10.1093/nar/gkl928
Publication status	Published - 2006

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Kuhn, R. M., Karolchik, D., Zweig, A. S., Trumbower, H., Thomas, D. J., Thakkapallayil, A., Sugnet, C. W., Stanke, M., Smith, K. E., Siepel, A., Rosenbloom, K. R., Rhead, B., Raney, B. J., Pohl, A., Pedersen, J. S., Hsu, F., Hinrichs, A. S., Harte, R. A., Diekhans, M., ... Kent, W. J. (2006). The UCSC genome browser database: update 2007. Nucleic Acids Research, 35(Database issue), D668-73. https://doi.org/10.1093/nar/gkl928

Kuhn, RM, Karolchik, D, Zweig, AS, Trumbower, H, Thomas, DJ, Thakkapallayil, A, Sugnet, CW, Stanke, M, Smith, KE, Siepel, A, Rosenbloom, KR, Rhead, B, Raney, BJ, Pohl, A, Pedersen, JS, Hsu, F, Hinrichs, AS, Harte, RA, Diekhans, M, Clawson, H, Bejerano, G, Barber, GP, Baertsch, R, Haussler, D & Kent, WJ 2006, 'The UCSC genome browser database: update 2007.', Nucleic Acids Research, vol. 35, no. Database issue, pp. D668-73. https://doi.org/10.1093/nar/gkl928

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title = "The UCSC genome browser database: update 2007.",

abstract = "The University of California, Santa Cruz Genome Browser Database contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up to a full chromosome and includes assembly data, genes and gene predictions, mRNA and EST alignments, and comparative genomics, regulation, expression and variation data. The database is optimized for fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. In the past year, 22 new assemblies and several new sets of human variation annotation have been released. New features include VisiGene, a fully integrated in situ hybridization image browser; phyloGif, for drawing evolutionary tree diagrams; a redesigned Custom Track feature; an expanded SNP annotation track; and many new display options. The Genome Browser, other tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.",

author = "Kuhn, {R M} and D Karolchik and Zweig, {A S} and H Trumbower and Thomas, {D J} and A Thakkapallayil and Sugnet, {C W} and M Stanke and Smith, {K E} and A Siepel and Rosenbloom, {K R} and B Rhead and Raney, {B J} and A Pohl and Pedersen, {Jakob Skou} and F Hsu and Hinrichs, {A S} and Harte, {R A} and M Diekhans and H Clawson and G Bejerano and Barber, {G P} and R Baertsch and D Haussler and Kent, {W J}",

note = "Keywords: Animals; Base Sequence; Cattle; Computer Graphics; Conserved Sequence; Databases, Genetic; Genome, Human; Genomics; Humans; Internet; Linkage Disequilibrium; Mice; Open Reading Frames; Polymorphism, Single Nucleotide; Rats; Regulatory Sequences, Nucleic Acid; User-Computer Interface",

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doi = "10.1093/nar/gkl928",

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AU - Kuhn, R M

AU - Karolchik, D

AU - Zweig, A S

AU - Trumbower, H

AU - Thomas, D J

AU - Thakkapallayil, A

AU - Sugnet, C W

AU - Stanke, M

AU - Smith, K E

AU - Siepel, A

AU - Rosenbloom, K R

AU - Rhead, B

AU - Raney, B J

AU - Pohl, A

AU - Pedersen, Jakob Skou

AU - Hsu, F

AU - Hinrichs, A S

AU - Harte, R A

AU - Diekhans, M

AU - Clawson, H

AU - Bejerano, G

AU - Barber, G P

AU - Baertsch, R

AU - Haussler, D

AU - Kent, W J

N1 - Keywords: Animals; Base Sequence; Cattle; Computer Graphics; Conserved Sequence; Databases, Genetic; Genome, Human; Genomics; Humans; Internet; Linkage Disequilibrium; Mice; Open Reading Frames; Polymorphism, Single Nucleotide; Rats; Regulatory Sequences, Nucleic Acid; User-Computer Interface

PY - 2006

Y1 - 2006

N2 - The University of California, Santa Cruz Genome Browser Database contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up to a full chromosome and includes assembly data, genes and gene predictions, mRNA and EST alignments, and comparative genomics, regulation, expression and variation data. The database is optimized for fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. In the past year, 22 new assemblies and several new sets of human variation annotation have been released. New features include VisiGene, a fully integrated in situ hybridization image browser; phyloGif, for drawing evolutionary tree diagrams; a redesigned Custom Track feature; an expanded SNP annotation track; and many new display options. The Genome Browser, other 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 contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up to a full chromosome and includes assembly data, genes and gene predictions, mRNA and EST alignments, and comparative genomics, regulation, expression and variation data. The database is optimized for fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. In the past year, 22 new assemblies and several new sets of human variation annotation have been released. New features include VisiGene, a fully integrated in situ hybridization image browser; phyloGif, for drawing evolutionary tree diagrams; a redesigned Custom Track feature; an expanded SNP annotation track; and many new display options. The Genome Browser, other tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.

U2 - 10.1093/nar/gkl928

DO - 10.1093/nar/gkl928

M3 - Journal article

C2 - 17142222

SN - 0305-1048

VL - 35

SP - D668-73

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - Database issue

ER -

The UCSC genome browser database: update 2007.

Abstract

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