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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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Ensembl release 46 page showing the gold-coloured Ensembl-Vega gene merge loci (top: Overview) and transcripts (bottom: Detailed view). Edited from http://www.ensembl.org/Homo_sapiens/contigview?c=1:39255078;w=63203.
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Figure 2: Ensembl release 46 page showing the gold-coloured Ensembl-Vega gene merge loci (top: Overview) and transcripts (bottom: Detailed view). Edited from http://www.ensembl.org/Homo_sapiens/contigview?c=1:39255078;w=63203.

Mentions: Vega transcript objects are also shown, in a separate track, in Ensembl Detailed View (tracks named ‘Vega Havana Gene’ and ‘Vega External Gene’; the user may have to switch these tracks on in the ‘Features’ menu). In order to eliminate redundancy in the Ensembl transcript track and highlight commonality, Ensembl and Vega have started to match protein-coding transcripts between the two datasets and only present a single transcript if within a given locus a Vega and an Ensembl transcript are identical. These transcripts (and loci containing them) are coloured gold and labelled ‘Merged Known Protein Coding’ or ‘Common Known Protein Coding’ in Ensembl ContigVew (Figure 2). The project is currently limited to human genes annotated by Havana, but is expected to include Havana-annotated mouse genes in Ensembl version 48 (December 2007 release).Figure 2.


The vertebrate genome annotation (Vega) database.

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

Ensembl release 46 page showing the gold-coloured Ensembl-Vega gene merge loci (top: Overview) and transcripts (bottom: Detailed view). Edited from http://www.ensembl.org/Homo_sapiens/contigview?c=1:39255078;w=63203.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: Ensembl release 46 page showing the gold-coloured Ensembl-Vega gene merge loci (top: Overview) and transcripts (bottom: Detailed view). Edited from http://www.ensembl.org/Homo_sapiens/contigview?c=1:39255078;w=63203.
Mentions: Vega transcript objects are also shown, in a separate track, in Ensembl Detailed View (tracks named ‘Vega Havana Gene’ and ‘Vega External Gene’; the user may have to switch these tracks on in the ‘Features’ menu). In order to eliminate redundancy in the Ensembl transcript track and highlight commonality, Ensembl and Vega have started to match protein-coding transcripts between the two datasets and only present a single transcript if within a given locus a Vega and an Ensembl transcript are identical. These transcripts (and loci containing them) are coloured gold and labelled ‘Merged Known Protein Coding’ or ‘Common Known Protein Coding’ in Ensembl ContigVew (Figure 2). The project is currently limited to human genes annotated by Havana, but is expected to include Havana-annotated mouse genes in Ensembl version 48 (December 2007 release).Figure 2.

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