The UCSC genome browser database: update 2007

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., Clawson, H., Bejerano, G., Barber, G. P., Baertsch, R., Haussler, D., Kent, W. J. (January 2007) The UCSC genome browser database: update 2007. Nucleic Acids Res, 35 (Databa). D668-73. ISSN 0305-1048

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DOI: 10.1093/nar/gkl928


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

Item Type: Paper
Uncontrolled 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
Subjects: bioinformatics
bioinformatics > genomics and proteomics > databases
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
CSHL Authors:
Communities: CSHL labs > Siepel lab
Depositing User: Matt Covey
Date: January 2007
Date Deposited: 14 Jan 2015 14:47
Last Modified: 08 Nov 2017 15:25
PMCID: PMC1669757
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