January 15-19, 2011
Town & Country Convention Center
San Diego, CA
Scott Cain1 , Ed Lee2 , Carson Holt3 , Stephen Ficklin4 , Meg Staton5 , Lincoln Stein1 , GMOD Consortium1
The costs associated with DNA sequencing have decreased considerably and the number of organisms having their genomes sequenced has increased. Several organizations have implemented methods for community annotation using tools from the Generic Model Organism Database (GMOD) project, including ParameciumDB, GnpAnnot, AphidBase, and BeeBase. Here we present an example system based entirely on GMOD tools for community annotation implemented in a VMware virtual machine that could, with little extra effort, be used directly for annotating a nascent genome. The tools include Chado (a genomics database schema), GBrowse (a web based genome browser), Apollo (a genome annotation tool), MAKER (a genome annotation pipeline), and Tripal (a Drupal-based content management system).