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. 2008 Jan;36(Database issue):D773-9.
doi: 10.1093/nar/gkm966. Epub 2007 Dec 17.

The UCSC Genome Browser Database: 2008 update

D Karolchik  1 , R M Kuhn, R Baertsch, G P Barber, H Clawson, M Diekhans, B Giardine, R A Harte, A S Hinrichs, F Hsu, K M Kober, W Miller, J S Pedersen, A Pohl, B J Raney, B Rhead, K R Rosenbloom, K E Smith, M Stanke, A Thakkapallayil, H Trumbower, T Wang, A S Zweig, D Haussler, W J Kent
Affiliations

The UCSC Genome Browser Database: 2008 update

D Karolchik et al. Nucleic Acids Res. 2008 Jan.

Abstract

The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrate and 21 invertebrate species as of September 2007. For each assembly, the GBD contains a collection of annotation data aligned to the genomic sequence. Highlights of this year's additions include a 28-species human-based vertebrate conservation annotation, an enhanced UCSC Genes set, and more human variation, MGC, and ENCODE data. The database is optimized for fast interactive performance with a set of web-based tools that may be used to view, manipulate, filter and download the annotation data. New toolset features include the Genome Graphs tool for displaying genome-wide data sets, session saving and sharing, better custom track management, expanded Genome Browser configuration options and a Genome Browser wiki site. The downloadable GBD data, the companion Genome Browser toolset and links to documentation and related information can be found at: http://genome.ucsc.edu/.

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Figures

Figure 1.
Figure 1.
Genome Graphs for the human May 2004 (Build 35, hg17) assembly loaded with data published by the Wellcome Trust Case Control Consortium from a genome-wide association study of seven common diseases (40).
Figure 2.
Figure 2.
A zoomed-in view of the human and non-human mRNA tracks in the chrX:151 572 101–151 572 240 region on the human March 2006 (Build 36, hg18) genome assembly. In both mRNA tracks, the mRNA coloring options are configured to show nonsynonymous codon differences between the mRNA alignments and the genomic feature at the top of the figure. Red indicates codons that differ from the human genomic sequence. The double horizontal lines in the ‘Non-Human mRNAs’ track highlight areas in which both the mRNA and the genome sequence have an insertion or stretch of non-matching sequence. Note the blue vertical line at the beginning of the bottom Rattus alignment, indicating an insertion at the beginning of the query sequence, also the orange vertical lines with partial peptide insertions in the Rattus alignments.
Figure 3.
Figure 3.
A zoomed-out view of human mRNA alignments in the chrX:153 229 581–153 304 741 region using ‘squish’ display mode and configured to show nonsynonymous codon differences between the human mRNAs and the genomic sequence. This view is useful for quickly scanning for mRNAs that are free of nonsynonymous regions (i.e. are all-black in color) and have a valid poly(A) tail (green vertical bar).
See this image and copyright information in PMC

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