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. 2007 Jan;35(Database issue):D668-73.
doi: 10.1093/nar/gkl928. Epub 2006 Nov 16.

The UCSC genome browser database: update 2007

R M Kuhn  1 , 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, J S 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
Affiliations

The UCSC genome browser database: update 2007

R M Kuhn et al. Nucleic Acids Res. 2007 Jan.

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/.

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Figures

Figure 1
Figure 1
Screenshot of VisiGene display for mouse Hoxa9 gene.
Figure 2
Figure 2
New display features. Region of HAR1 gene on chromosome 20 (37). Blue or gray mini-button on the left affords access to track configuration. mRNA track: red ticks, bases differ from reference; double arrows navigate to next exon. Conservation track: yellow, aligning sequence has missing data; double lines, unaligned DNA exists on both reference and aligning species; blue tick in opossum track, end of synteny block.
See this image and copyright information in PMC

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References

    1. Kent W.J., Sugnet C.W., Furey T.S., Roskin K.M., Pringle T.H., Zahler A.M., Haussler D. The human genome browser at UCSC. Genome Res. 2002;12:996–1006. - PMC - PubMed
    1. Hinrichs A.S., Karolchik D., Baertsch R., Barber G.P., Bejerano G., Clawson H., Diekhans M., Furey T.S., Harte R.A., Hsu F., et al. The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. 2006;34:D590–D598. - PMC - PubMed
    1. Kent W.J. BLAT—the BLAST-like alignment tool. Genome Res. 2002;12:656–664. - PMC - PubMed
    1. Kent W.J., Hsu F., Karolchik D., Kuhn R.M., Clawson H., Trumbower H., Haussler D. Exploring relationships and mining data with the UCSC Gene Sorter. Genome Res. 2005;15:737–741. - PMC - PubMed
    1. Hsu F., Pringle T.H., Kuhn R.M., Karolchik D., Diekhans M., Haussler D., Kent W.J. The UCSC Proteome Browser. Nucleic Acids Res. 2005;33:D454–D458. - PMC - PubMed

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