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The vertebrate genome annotation (Vega) database.

Wilming LG, Gilbert JG, Howe K, Trevanion S, Hubbard T, Harrow JL - Nucleic Acids Res. (2007)

Bottom Line: The Vertebrate Genome Annotation (Vega) database (http://vega.sanger.ac.uk) was first made public in 2004 and has been designed to view manual annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute.Since its initial release, the number of human annotated loci has more than doubled to close to 33 000 and now contains comprehensive annotation on 20 of the 24 human chromosomes, four whole mouse chromosomes and around 40% of the zebrafish Danio rerio genome.In addition, we offer manual annotation of a number of haplotype regions in mouse and human and regions of comparative interest in pig and dog that are unique to Vega.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. lw2@sanger.ac.uk

ABSTRACT
The Vertebrate Genome Annotation (Vega) database (http://vega.sanger.ac.uk) was first made public in 2004 and has been designed to view manual annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute. Since its initial release, the number of human annotated loci has more than doubled to close to 33 000 and now contains comprehensive annotation on 20 of the 24 human chromosomes, four whole mouse chromosomes and around 40% of the zebrafish Danio rerio genome. In addition, we offer manual annotation of a number of haplotype regions in mouse and human and regions of comparative interest in pig and dog that are unique to Vega.

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Zebrafish haplotype clones are marked in yellow (Top level and Navigational overview panels above). In MultiContigView, annotation can be shown on both reference and haplotype simultaneously with lines linking homologous genes (Detailed View panel above). This view is accessible by choosing the desired second dataset from the ‘View alongside’ menu from the left-hand menu/navigation bar in ContigView (not shown). Edited from http://vega.sanger.ac.uk/Danio_rerio/multicontigview?sr1=H_4_11;s1=Danio_rerio;c=4:8468245;w=44415.
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Figure 3: Zebrafish haplotype clones are marked in yellow (Top level and Navigational overview panels above). In MultiContigView, annotation can be shown on both reference and haplotype simultaneously with lines linking homologous genes (Detailed View panel above). This view is accessible by choosing the desired second dataset from the ‘View alongside’ menu from the left-hand menu/navigation bar in ContigView (not shown). Edited from http://vega.sanger.ac.uk/Danio_rerio/multicontigview?sr1=H_4_11;s1=Danio_rerio;c=4:8468245;w=44415.

Mentions: In preparation for the zebrafish genome paper (which will be based on genome assembly Zv8), all mRNA entries in the Zfin database (http://zfin.org/) have been aligned to the current Zv7 assembly and those that map have been annotated (currently 6157). On an ongoing basis, known mRNAs are being mapped and annotated as new finished genomic sequence becomes available. To remove artificial duplications, annotation from the previous mixed-strain library genomic clones has been moved to a reference assembly constructed from a single double-haplotype Tübingen strain individual. The original clones are still visible in ContigView and annotation can be compared between the two in MultiContigView (Figure 3) using the ‘Comparative’ menu in Detailed View.Figure 3.


The vertebrate genome annotation (Vega) database.

Wilming LG, Gilbert JG, Howe K, Trevanion S, Hubbard T, Harrow JL - Nucleic Acids Res. (2007)

Zebrafish haplotype clones are marked in yellow (Top level and Navigational overview panels above). In MultiContigView, annotation can be shown on both reference and haplotype simultaneously with lines linking homologous genes (Detailed View panel above). This view is accessible by choosing the desired second dataset from the ‘View alongside’ menu from the left-hand menu/navigation bar in ContigView (not shown). Edited from http://vega.sanger.ac.uk/Danio_rerio/multicontigview?sr1=H_4_11;s1=Danio_rerio;c=4:8468245;w=44415.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238886&req=5

Figure 3: Zebrafish haplotype clones are marked in yellow (Top level and Navigational overview panels above). In MultiContigView, annotation can be shown on both reference and haplotype simultaneously with lines linking homologous genes (Detailed View panel above). This view is accessible by choosing the desired second dataset from the ‘View alongside’ menu from the left-hand menu/navigation bar in ContigView (not shown). Edited from http://vega.sanger.ac.uk/Danio_rerio/multicontigview?sr1=H_4_11;s1=Danio_rerio;c=4:8468245;w=44415.
Mentions: In preparation for the zebrafish genome paper (which will be based on genome assembly Zv8), all mRNA entries in the Zfin database (http://zfin.org/) have been aligned to the current Zv7 assembly and those that map have been annotated (currently 6157). On an ongoing basis, known mRNAs are being mapped and annotated as new finished genomic sequence becomes available. To remove artificial duplications, annotation from the previous mixed-strain library genomic clones has been moved to a reference assembly constructed from a single double-haplotype Tübingen strain individual. The original clones are still visible in ContigView and annotation can be compared between the two in MultiContigView (Figure 3) using the ‘Comparative’ menu in Detailed View.Figure 3.

Bottom Line: The Vertebrate Genome Annotation (Vega) database (http://vega.sanger.ac.uk) was first made public in 2004 and has been designed to view manual annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute.Since its initial release, the number of human annotated loci has more than doubled to close to 33 000 and now contains comprehensive annotation on 20 of the 24 human chromosomes, four whole mouse chromosomes and around 40% of the zebrafish Danio rerio genome.In addition, we offer manual annotation of a number of haplotype regions in mouse and human and regions of comparative interest in pig and dog that are unique to Vega.

View Article: PubMed Central - PubMed

Affiliation: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. lw2@sanger.ac.uk

ABSTRACT
The Vertebrate Genome Annotation (Vega) database (http://vega.sanger.ac.uk) was first made public in 2004 and has been designed to view manual annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute. Since its initial release, the number of human annotated loci has more than doubled to close to 33 000 and now contains comprehensive annotation on 20 of the 24 human chromosomes, four whole mouse chromosomes and around 40% of the zebrafish Danio rerio genome. In addition, we offer manual annotation of a number of haplotype regions in mouse and human and regions of comparative interest in pig and dog that are unique to Vega.

Show MeSH