New Tools for Manual Genome Annotation in Eukaryotes: Zmap/Otterlace and Vega

The HAVANA group produces manually annotated gene sets for a number of vertebrate genomes, including the reference GENCODE gene sets for human and mouse. We also provide the research community with the necessary training and access to our software so that annotation can be performed remotely by external collaborators to generate their own gene sets. Using this methodology we have successfully undertaken community annotation projects in pig (Dawson et al 2013) and are currently working on a similar project with rat.

Our software, Zmap/Otterlace, is available as a Mac or Linux client, which communicates with our server over HTTP, and enables annotators to work anywhere as long as they can connect to the Sanger web server. The server controls data access and allows multi-user annotation, whilst the client holds a local copy of the section of genome that is being annotated. Genomic sequence is run though our custom analysis pipeline and this is displayed in our graphical visualisation tool Zmap, which communicates with Otterlace to create and store the annotation.

The resulting annotation is either subject to quality control internally by experienced annotators (Gatekeeper model) or deposited directly once the annotator has received sufficient training (Blessed annotator model) (Loveland et al 2012). The approved gene sets are hosted on the Vega genome browser (http://vega.sanger.ac.uk/). We follow the Ensembl quarterly release cycle, however a customised update track is available which expedites the fast public release of genes of interest. Our annotation software is freely available via our website (http://www.sanger.ac.uk/resources/software/otterlace/).

References:

Loveland JE et al. PMID:22434843

Dawson HD et al. PMID:23676093