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).
Highlights
In 2014, the Vertebrate Genome Annotation (VEGA) browser will celebrate its 10th anniversary. It was initially designed as a community resource for browsing manual annotation, produced by the Human And Vertebrate Analysis aNd Annotation (HAVANA) team based at the Wellcome Trust Sanger Institute (WTSI), of finished sequence from the Human Genome Project (HGP) [1]
It was thought that the manual annotation may not be needed past the completion of the human reference genome and that automated gene builds provided by Ensembl may be sufficient for the researchers needs
To examine the consequence of single nucleotide variation (SNV) on the structure of transcripts, as part of the study by MacArthur et al [19] to identify all loss of function (LoF) variation in human protein-coding genes, we manually annotated the transcript models associated with 884 putative LoF variants to help users to visualize the SNV consequences
Summary
In 2014, the Vertebrate Genome Annotation (VEGA) (http://vega.sanger.ac.uk) browser will celebrate its 10th anniversary. It was thought that the manual annotation may not be needed past the completion of the human reference genome and that automated gene builds provided by Ensembl may be sufficient for the researchers needs. In terms of the annotation data themselves, for the primary species (human, mouse, zebrafish and pig) they are presented first in VEGA and in Ensembl, both as distinct gene sets in the browser itself and as part of the Ensembl merged gene set.
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
