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. 2003 Jan 1;31(1):51-4.
doi: 10.1093/nar/gkg129.

The UCSC Genome Browser Database

D Karolchik  1 , R Baertsch, M Diekhans, T S Furey, A Hinrichs, Y T Lu, K M Roskin, M Schwartz, C W Sugnet, D J Thomas, R J Weber, D Haussler, W J Kent; University of California Santa Cruz
Affiliations

The UCSC Genome Browser Database

D Karolchik et al. Nucleic Acids Res. .

Abstract

The University of California Santa Cruz (UCSC) Genome Browser Database is an up to date source for genome sequence data integrated with a large collection of related annotations. The database is optimized to support fast interactive performance with the web-based UCSC Genome Browser, a tool built on top of the database for rapid visualization and querying of the data at many levels. The annotations for a given genome are displayed in the browser as a series of tracks aligned with the genomic sequence. Sequence data and annotations may also be viewed in a text-based tabular format or downloaded as tab-delimited flat files. The Genome Browser Database, browsing tools and downloadable data files can all be found on the UCSC Genome Bioinformatics website (http://genome.ucsc.edu), which also contains links to documentation and related technical information.

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Figures

Figure 1
Figure 1
Screenshot of the Genome Browser annotation tracks display showing a view of an entire chromosome, human chr7 from the June 28, 2002 assembly. This level of detail provides an overview of the coverage and completeness for the region. The red section in the Chromosome Band track indicates the centromere. The shading in the Coverage track shows finished areas and coverage depth in draft areas. The Gap track indicates gaps in the assembly. The RefSeq Genes track shows gene density.
Figure 2
Figure 2
A zoomed-in view of the same chromosome shown in Figure 1. The finer level of detail pinpoints the location of individual features in the annotation tracks. In the mRNA and RefSeq Genes gene prediction tracks, aligning regions (usually coding exons) are depicted by blocks connected by thin horizontal lines representing gaps (usually spliced-out introns). Thinner blocks on the leading and trailing ends of the aligning regions depict the 5′ and 3′ untranslated regions (UTRs). Arrowheads on the connecting lines show the direction of transcription.
See this image and copyright information in PMC

References

    1. International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860–921. - PubMed
    1. Kent W.J., Sugnet,C.W., Furey,T.S., Roskin,K.M., Pringle,T.H., Zahler,A.M. and Haussler,D. (2002) The Human Genome Browser at UCSC. Genome Res., 12, 996–1006. - PMC - PubMed
    1. Kent W.J. and Brumbaugh,H. (2002) autoSql and autoXml: Code Generators from the Genome Project. Linux J., 99, 68–77.
    1. Kent W.J. (2002) BLAT—the BLAST-like alignment tool. Genome Res., 12, 656–664. - PMC - PubMed
    1. Hubbard T., Barker,D., Birney,E., Cameron,G., Chen,Y., Clark,L., Cox,T., Cuff,J., Curwen,V., Down,T., Durbin,R., Eyras,E., Gilbert,J., Hammond,M., Huminiecki,L., Kasprzyk,A., Lehvaslaiho,H., Lijnzaad,P., Melsopp,C., Mongin,E., Pettett,R., Pocock,M., Potter,S., Rust,A., Schmidt,E., Searle,S., Slater,G., Smith,J., Spooner,W., Stabenau,A., Stalker,J., Stupka,E., Ureta-Vidal,A., Vastrik,I. and Clamp,M. (2002) The Ensembl genome database project. Nucleic Acids Res., 30, 38–41. - PMC - PubMed

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