Manual Genome Annotation and Vega

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 and also annotate specific regions of interest such as dog (DLA), wallaby (MHC), Tasmanian devil (MHC), chimpanzee (MHC) and gorilla (MHC and LRC). The HAVANA team produces the manual annotation that is integrated into the GENCODE reference gene set for human and mouse which is displayed in both the Ensembl and UCSC genome browsers and can be downloaded from www.gencodegenes.org.

The Otterlace/Zmap annotation tools used by HAVANA were developed at the WTSI and are also used by external collaborators for community annotation. We have held cow, Xenopus tropicalis and pig annotation jamborees that have utilised these tools to generate high quality manual annotation for these organisms. Over 10% of the pig genome has been manually annotated in this way as part of the Immune Response Annotation Group (IRAG) community annotation effort on unfinished pig genomic sequence. We are also currently annotating the rat genome and have so far annotated over 1100 genes selected by the rat community.

All of our manual annotation is publicly available via Vega website (www.vega.sanger.ac.uk) and has also been merged with the Ensembl annotation as part of the merged Ensembl/Havana gene set.