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The UCSC Genome Browser Database: 2008 update.

Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F, Kober KM, Miller W, Pedersen JS, Pohl A, Raney BJ, Rhead B, Rosenbloom KR, Smith KE, Stanke M, Thakkapallayil A, Trumbower H, Wang T, Zweig AS, Haussler D, Kent WJ - Nucleic Acids Res. (2007)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA. donnak@soe.ucsc.edu

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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Related in: MedlinePlus

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.
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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.

Mentions: We have expanded the coloring and display options for mRNA tracks to include several ways to highlight gaps in alignments of query sequences (usually transcripts) to the genome, which frequently indicate a problem with the query sequence or with the genome assembly. Tracks may be colored by genomic, mRNA or nonsynonymous mRNA codons, mRNA bases, or different mRNA bases. Tracks may then be configured, through options on the description page, to display double horizontal lines at locations where both the genome and query sequence have an insertion and to display vertical lines of different colors to distinguish poly(A) tail insertions and insertions at the beginning, end or middle of the query (Figure 2). The new coloring scheme makes it easier to visually scan a region with hundreds of alignments and pick out regions of interest (Figure 3). The new display options are explained in detail on the mRNA track description pages.Figure 2.


The UCSC Genome Browser Database: 2008 update.

Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F, Kober KM, Miller W, Pedersen JS, Pohl A, Raney BJ, Rhead B, Rosenbloom KR, Smith KE, Stanke M, Thakkapallayil A, Trumbower H, Wang T, Zweig AS, Haussler D, Kent WJ - Nucleic Acids Res. (2007)

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.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238835&req=5

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.
Mentions: We have expanded the coloring and display options for mRNA tracks to include several ways to highlight gaps in alignments of query sequences (usually transcripts) to the genome, which frequently indicate a problem with the query sequence or with the genome assembly. Tracks may be colored by genomic, mRNA or nonsynonymous mRNA codons, mRNA bases, or different mRNA bases. Tracks may then be configured, through options on the description page, to display double horizontal lines at locations where both the genome and query sequence have an insertion and to display vertical lines of different colors to distinguish poly(A) tail insertions and insertions at the beginning, end or middle of the query (Figure 2). The new coloring scheme makes it easier to visually scan a region with hundreds of alignments and pick out regions of interest (Figure 3). The new display options are explained in detail on the mRNA track description pages.Figure 2.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA. donnak@soe.ucsc.edu

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/.

Show MeSH
Related in: MedlinePlus