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. 2012 Jan;40(Database issue):D918-23.
doi: 10.1093/nar/gkr1055. Epub 2011 Nov 15.

The UCSC Genome Browser Database: Extensions and Updates 2011

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Free PMC article

The UCSC Genome Browser Database: Extensions and Updates 2011

Timothy R Dreszer et al. Nucleic Acids Res. .
Free PMC article

Abstract

The University of California Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic data sets. In the past year, the local database has been updated with four new species assemblies, and we anticipate another four will be released by the end of 2011. Further, a large number of annotation tracks have been either added, updated by contributors, or remapped to the latest human reference genome. Among these are new phenotype and disease annotations, UCSC genes, and a major dbSNP update, which required new visualization methods. Growing beyond the local database, this year we have introduced 'track data hubs', which allow the Genome Browser to provide access to remotely located sets of annotations. This feature is designed to significantly extend the number and variety of annotation tracks that are publicly available for visualization and analysis from within our site. We have also introduced several usability features including track search and a context-sensitive menu of options available with a right-click anywhere on the Browser's image.

Figures

Figure 1.
Figure 1.
A simple search has been performed to find annotation tracks related to disease phenotype. One of the search results is a container of related tracks.
Figure 2.
Figure 2.
Annotation tracks from OMIM, dbSNP, UCSC Genes, ENCODE Histone HMM and the Epigenomics Roadmap data hub combined in one image. The new context-sensitive menu is shown with the highlighted track about to be configured.

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References

    1. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res. 2002;12:996–1006. - PMC - PubMed
    1. Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, et al. The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 2011;39:D876–D882. - PMC - PubMed
    1. McPherson JD, Marra M, Hillier L, Waterston RH, Chinwalla A, Wallis J, Sekhon M, Wylie K, Mardis ER, Wilson RK, et al. A physical map of the human genome. Nature. 2001;409:934–941. - PubMed
    1. Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ, et al. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res. 2009;18:1316–1323. - PMC - PubMed
    1. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2011;39:D32–D37. - PMC - PubMed

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