- The Vertebrate Genome Annotation browser 10 years on. [PMID: 24316575]
Jennifer L Harrow, Charles A Steward, Adam Frankish, James G Gilbert, Jose M Gonzalez, Jane E Loveland, Jonathan Mudge, Dan Sheppard, Mark Thomas, Stephen Trevanion, Laurens G Wilming
Nucleic acids research 2014:42(Database issue)
16 Citations (Google Scholar as of 2016-02-27)
Abstract: The Vertebrate Genome Annotation (VEGA) database (http://vega.sanger.ac.uk), initially designed as a community resource for browsing manual annotation of the human genome project, now contains five reference genomes (human, mouse, zebrafish, pig and rat). Its introduction pages have been redesigned to enable the user to easily navigate between whole genomes and smaller multi-species haplotypic regions of interest such as the major histocompatibility complex. The VEGA browser is unique in that annotation is updated via the Human And Vertebrate Analysis aNd Annotation (HAVANA) update track every 2 weeks, allowing single gene updates to be made publicly available to the research community quickly. The user can now access different haplotypic subregions more easily, such as those from the non-obese diabetic mouse, and display them in a more intuitive way using the comparative tools. We also highlight how the user can browse manually annotated updated patches from the Genome Reference Consortium (GRC).
- The vertebrate genome annotation (Vega) database. [PMID: 18003653]
L G Wilming, J G R Gilbert, K Howe, S Trevanion, T Hubbard, J L Harrow
Nucleic acids research 2008:36(Database issue)
195 Citations (Google Scholar as of 2016-02-27)
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.
- The Vertebrate Genome Annotation (Vega) database. [PMID: 15608237]
J L Ashurst, C-K Chen, J G R Gilbert, K Jekosch, S Keenan, P Meidl, S M Searle, J Stalker, R Storey, S Trevanion, L Wilming, T Hubbard
Nucleic acids research 2005:33(Database issue)
157 Citations (Google Scholar as of 2016-02-27)
Abstract: The Vertebrate Genome Annotation (Vega) database (http://vega.sanger.ac.uk) has been designed to be a community resource for browsing manual annotation of finished sequences from a variety of vertebrate genomes. Its core database is based on an Ensembl-style schema, extended to incorporate curation-specific metadata. In collaboration with the genome sequencing centres, Vega attempts to present consistent high-quality annotation of the published human chromosome sequences. In addition, it is also possible to view various finished regions from other vertebrates, including mouse and zebrafish. Vega displays only manually annotated gene structures built using transcriptional evidence, which can be examined in the browser. Attempts have been made to standardize the annotation procedure across each vertebrate genome, which should aid comparative analysis of orthologues across the different finished regions.