Manual Genome Annotation

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 annotated across whole genomes for human, mouse, zebrafish, pig and rat and specific regions of interest, such as the Major Histocompatibility Complex (MHC), for selected organisms. The annotation comprises protein coding genes, long non-coding RNAs, pseudogenes and other specialised biotypes such as Immunoglobulin and T-cell receptor genes. Our manual annotation is publicly available from the Vertebrate Genome Annotation Database (VEGA) (www.vega.sanger.ac.uk) and is merged with the automated Ensembl annotation to produce the GENCODE gene set for human and mouse. The annotation can be downloaded from gencodegenes.org and is available from the Ensembl and UCSC genome browsers.

In addition to active annotation of human and mouse, we are currently working on the transfer of the manual annotation of the pig WTSI-X chromosome to produce a merged gene set for the new Sus_scrofa-X 11 chromosome. The WTSI-Y chromosome and its manual annotation will be incorporated in to the Sus_scrofa 11 genome release in Ensembl, which is due May 2017.

Manual annotation is a major part of Ensembl and the GENCODE gene set. Annotation is a continuous process and so between the regular releases of the Ensembl/GENCODE update cycle we release new annotation every 24 hours via an update track hub that can be accessed from all genome browsers and is available here: ftp://ngs.sanger.ac.uk/production/gencode/update_trackhub/hub.txt