Plant & Animal Genomes XIX Conference

January 15-19, 2011
Town & Country Convention Center
San Diego, CA

A Complete Community Annotation System Using GMOD Tools

Scott Cain¹ , Ed Lee² , Carson Holt³ , Stephen Ficklin⁴ , Meg Staton⁵ , Lincoln Stein¹ , GMOD Consortium¹

¹  Ontario Institute for Cancer Research, Toronto, Ontario, Canada, M5G 0A3

²  Lawrence Berkeley National Lab, Berkeley, CA 94720

³  University of Utah, Salt Lake City, UT 84112

⁴  Washington State University, Pullman, WA, 99164

⁵  Clemson University Genomics Institute, Clemson, SC 29634

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).