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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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Part of the GeneView Locus Report showing versioning information and CCDS and nomenclature (in this case HGNC) information and links. Edited from http://vega.sanger.ac.uk/Homo_sapiens/geneview?gene=OTTHUMG00000008264&db=core.
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Figure 1: Part of the GeneView Locus Report showing versioning information and CCDS and nomenclature (in this case HGNC) information and links. Edited from http://vega.sanger.ac.uk/Homo_sapiens/geneview?gene=OTTHUMG00000008264&db=core.

Mentions: All three complete genomes (mouse, human and zebrafish) now contain a view of all the chromosomes in the Karyotype View and the annotation progress of each chromosome is highlighted with grey shading. Since the original Vega publication in 2005 (2), the number of human gene loci annotated has more than doubled to almost 33 000 (June 2007 release), close to 19 000 of which are predicted to be protein coding. Four chromosomes (2, 4, 5 and 11) remain to be fully manually annotated to the Havana standard and these will be completed as part of the CCDS collaboration and the whole-genome extension of the ENCODE project (see below). Since annotation is continually re-evaluated on a gene-by-gene basis, every locus is versioned and the date of creation and last update can now be viewed by the user on the curated locus report page (GeneView, see Figure 1).Figure 1.


The vertebrate genome annotation (Vega) database.

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

Part of the GeneView Locus Report showing versioning information and CCDS and nomenclature (in this case HGNC) information and links. Edited from http://vega.sanger.ac.uk/Homo_sapiens/geneview?gene=OTTHUMG00000008264&db=core.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: Part of the GeneView Locus Report showing versioning information and CCDS and nomenclature (in this case HGNC) information and links. Edited from http://vega.sanger.ac.uk/Homo_sapiens/geneview?gene=OTTHUMG00000008264&db=core.
Mentions: All three complete genomes (mouse, human and zebrafish) now contain a view of all the chromosomes in the Karyotype View and the annotation progress of each chromosome is highlighted with grey shading. Since the original Vega publication in 2005 (2), the number of human gene loci annotated has more than doubled to almost 33 000 (June 2007 release), close to 19 000 of which are predicted to be protein coding. Four chromosomes (2, 4, 5 and 11) remain to be fully manually annotated to the Havana standard and these will be completed as part of the CCDS collaboration and the whole-genome extension of the ENCODE project (see below). Since annotation is continually re-evaluated on a gene-by-gene basis, every locus is versioned and the date of creation and last update can now be viewed by the user on the curated locus report page (GeneView, see Figure 1).Figure 1.

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