The Vertebrate Genome Annotation Database (VEGA) and Community Manual Annotation

The Human and Vertebrate Analysis and Annotation (HAVANA) team at the Wellcome Trust Sanger Institute (WTSI) undertakes manual annotation of finished vertebrate genomic sequence.  We also annotate specific regions of interest, such as pig (SLA and LRC), dog (DLA), wallaby (MHC) and gorilla (MHC and LRC).  Our manual annotation is publicly available from the Vertebrate Genome Annotation Database (VEGA) (www.vega.sanger.ac.uk). The HAVANA group contributes to the ENCODE project producing the manual annotation integrated in the GENCODE reference gene set. The GENCODE gene set is displayed in both the Ensembl and UCSC genome browsers and can be downloaded from gencodegenes.org.  This gene set is updated every three months and release 15 should contain a full first-pass manual annotation of the whole genome.

Annotation tools that have been developed at the WTSI  (Otterlace/Zmap) are being used remotely by external collaborators for community annotation. This “Blessed” annotator and “Gatekeeper” approach to community annotation is being used in mouse and pig respectively. We have annotated over 10% of the pig genome as part of the Immune Response Annotation Group in a community annotation effort on unfinished pig genomic sequence. The Vega website has been recently updated to pig build 10.2 and includes the manually annotated genes from the IRAG group. This annotation is shortly to be merged with the Ensembl annotation as part of the merged Ensembl/Havana gene set. At WTSI we have also sequenced the pig X and Y chromosomes and are completing their annotation.