Community 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 specific regions of interest, such as the Major Histocompatibility Complex (MHC), for selected organisms). 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 for human and mouse. This can be downloaded from gencodegenes.org and is available from the Ensembl and UCSC genome browsers.

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 annotation workshops for several species, most recently rat, that have utilised these tools and generated high quality manual annotation. To date have annotated over 2200 genes chosen by the rat community. Gene clusters are particular targets for manual annotation due to the difficulty with their automated annotation. We recently completed the annotation of the MHC (RT1) region in rat.

Annotation is a continuous process and so between database updates we can release new annotation via a Vega update track for all of our whole genome species.

http://vega.sanger.ac.uk/info/data/frequent_update.html

If you have any queries please contact us at:

vega-helpdesk@sanger.ac.uk