The Vertebrate Genome Annotation Database (VEGA) and the Use of Otterlace As a Community Annotation Tool

The Human and Vertebrate Analysis and Annotation (HAVANA) team at the Wellcome Trust Sanger Institute (WTSI) undertakes manual annotation of vertebrate genomic sequence.  We have whole genomes for human, mouse, zebrafish, pig and rat. We also annotate specific regions of interest, such as pig (SLA and LRC), dog (DLA), wallaby (MHC), Tasmanian devil (MHC), chimpanzee (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 team produces the manual annotation that is  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.

The Otterlace/Zmap annotation tools that have been developed at the WTSI, are being used remotely by external collaborators for community annotation. We have held cow, Xenopus tropicalis  and pig annotation jamborees that have utilised these tools and generated high quality manual annotation. Over 10% of the pig genome has been manually annotated as part of the Immune Response Annotation Group (IRAG) in a community annotation effort on unfinished pig genomic sequence. This annotation is available from the Vega website and has also been 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. Our annotation tools have been made available to the sheep genome community in tandem with RNAseq models from Ensembl to help refine their gene annotation.