VEGA Genome Browser

VEGA Genome Browser

VEGA Genome Browser

Overview

The Vertebrate Genome Annotation (VEGA) database 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.

Download and Installation

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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.

VEGA can be accessed here: http://vega.sanger.ac.uk

Contact

Publications

  • The Vertebrate Genome Annotation browser 10 years on.

    Harrow JL, Steward CA, Frankish A, Gilbert JG, Gonzalez JM et al.

    Nucleic acids research 2014;42;Database issue;D771-9

  • Community gene annotation in practice.

    Loveland JE, Gilbert JG, Griffiths E and Harrow JL

    Database : the journal of biological databases and curation 2012;2012;bas009