Plant & Animal Genomes XI Conference Plant & Animal Genomes XI ConferenceJanuary 11-15, 2003
Town & Country Convention Center
San Diego, CA
Workshop: Bioinformatics Interfaces, Ontologies and Interoperability
Gramene (www.gramene.org) is a web-based comparative genome-mapping database for the grasses funded by the USDA. The project seeks to provide an integrative set of web-based tools for discovery in agricultural genomics and to develop software applications for the bioinformatics community. The first reusable component from Gramene is a comparative mapping tool, Cmap. Cmap is a web-based application for displaying genetic and physical maps and their associated features. The tool provides a web-based interface for viewing comparative maps based upon a set of marker correspondences, a web-based interface for uploading datasets, and a simple schema currently compatible with MySQL, Oracle, and Sybase. For the web-based user, features of Cmap include the ability to display multiple maps, to find maps based on a known map study, their containing a particular feature, or by the number of contact points in common between two maps. Other features include the ability to display detailed pages within Cmap, and to provide external links to databases such as Genbank or Gramene. For the data provider, features of CMap include reliance on readily available open source components, simple installation, flexible configuration, and easy integration with other components of a model organism system web site. Cmap is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org.