The UCSC Genome Browser Database: 2008 update.
paper
Cited
Public
- Authors
- Karolchik, D; Kuhn, R M; Baertsch, R; Barber, G P; Clawson, H; Diekhans, M; Giardine, B; Harte, R A; Hinrichs, A S; Hsu, F; Kober, K M; Miller, W; Pedersen, J S; Pohl, A; Raney, B J; Rhead, B; Rosenbloom, K R; Smith, K E; Stanke, M; Thakkapallayil, A; Trumbower, H; Wang, T; Zweig, A S; Haussler, D; Kent, W J
- Year
- 2008
- Journal
- Nucleic acids research
- PMID
- 18086701
- DOI
- 10.1093/nar/gkm966
- PMCID
- PMC2238835
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/.
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).
A zoomed-in view of the human and non-human mRNA tracks in the chrX:151 572 101β151 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 βNon-Human mRNAsβ 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.
A zoomed-out view of human mRNA alignments in the chrX:153 229 581β153 304 741 region using βsquishβ 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).
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| Recent developments in StemBase: a tool to study gene expression in human and murine stem cells. | Sandie R et al. | β | 2009 | β |
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| Short Promoters in Viral Vectors Drive Selective Expression in Mammalian Inhibitory Neurons, but do not Restrict Activity to Specific Inhibitory Cell-Types. | Nathanson JL et al. | β | 2009 | β |
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| SNPit: a federated data integration system for the purpose of functional SNP annotation. | Shen TH et al. | β | 2009 | β |
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| Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. | Sanford JR et al. | β | 2009 | β |
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| The apolipoprotein L family of programmed cell death and immunity genes rapidly evolved in primates at discrete sites of host-pathogen interactions. | Smith EE et al. | β | 2009 | β |
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