VEGA (The Vertebrate Genome Annotation Database)

VEGA, the Vertebrate Genome Annotation Database, houses high-quality manual annotation of finished vertebrate genomic sequences. Manual annotation is currently more accurate at identifying splice variants, pseudogenes, polyadenylation [poly(A)] features, non-coding genes and complex gene arrangements and clusters than automated methods.

VEGA is built on the Ensembl database, which displays computationally curated sequences for a large number of vertebrate and invertebrate species. In contrast to the automatically generated annotation in Ensembl, the sequence annotation stored in VEGA is the result of manual annotation led by the Wellcome Trust Sanger Institute's HAVANA group and also displays manual annotation from other sequencing centres. The HAVANA and VEGA projects are led by Jen Harrow.

[Genome Research Limited]

Overview

VEGA was established in 2004 to provide a browser for viewing high-quality manual annotation of human and other vertebrate finished genomic sequences. High-quality annotation of the kind stored in the VEGA database provides an invaluable and reliable reference resource that can be used by researchers worldwide to predict gene structures on low-coverage genomes from other vertebrate species.

The HAVANA group is manually annotating the entire human genome and those of mouse and zebrafish (model organisms). This information is available via the VEGA browser and contains full manual annotation for 21 of the 24 human chromosomes. This work will be finished as part of the ENCODE project. Annotation of the mouse genome is being carried out as part of the mouse knockout project (EUCOMM/KOMP/NORCOMM), while annotation of the whole zebrafish genome is being conducted in collaboration with Zfin.

Because of their importance in the function of the immune system and autoimmunity, the Major Histocompatability Complex (MHC) regions of the gorilla, wallaby, pig and dog have also been manually annotated.

VEGA data are made freely and publicly available to all. Registered users are also able to save information, and customise the workspace shared with their groups.

Annotations displayed in VEGA are mirrored in the Ensembl database - provided the assemblies in the two databases are consistent.

Queries concerning Vega can be submitted to vega@sanger.ac.uk

Selected Publications

  • The vertebrate genome annotation (Vega) database.

    Wilming LG, Gilbert JG, Howe K, Trevanion S, Hubbard T and Harrow JL

    Nucleic acids research 2008;36;Database issue;D753-60

    PUBMED: 18003653; PMC: 2238886; DOI: 10.1093/nar/gkm987

  • VEGA, the genome browser with a difference.

    Loveland J

    Briefings in bioinformatics 2005;6;2;189-93

    PUBMED: 15975227

  • The Vertebrate Genome Annotation (Vega) database.

    Ashurst JL, Chen CK, Gilbert JG, Jekosch K, Keenan S, Meidl P, Searle SM, Stalker J, Storey R, Trevanion S, Wilming L and Hubbard T

    Nucleic acids research 2005;33;Database issue;D459-65

    PUBMED: 15608237; PMC: 540089; DOI: 10.1093/nar/gki135

  • The otter annotation system.

    Searle SM, Gilbert J, Iyer V and Clamp M

    Genome research 2004;14;5;963-70

    PUBMED: 15123593; PMC: 479127; DOI: 10.1101/gr.1864804

* quick link - http://q.sanger.ac.uk/vega