INTEGRATING RICEGENES AND SOYBASE GENETIC MAP AND SEQUENCE DATA FOR COMPARATIVE GENOMICS STUDIES

¹ Computational Biology Centers, University of Minnesota, Mayo Box 43, 420 Delaware St. SE, Minneapolis, MN 55455 USA

² Department of Plant Breeding, Cornell University

³ USDA-ARS and Department of Plant Breeding, Cornell University

⁴ Theory Center, Cornell University

⁵ USDA-ARS and Department of Agronomy, Iowa State University

⁶ USDA-ARS and Iowa State University

In an effort to facilitate comparative genomics studies using genetic map and sequence data, we are developing a computer system that combines several independent data sources together into a single data source with complex analysis capabilities. We are using an object-relational database management system (DBMS) to house genetic map data and EST, cDNA, and full-genome sequence data from several plant genomes. Placing these data together and providing tools for analysis and visualization will enable researchers to study, compare, and formulate hypotheses about the organization of genes on the chromosomes of various plant species. The initial step in the creation of this comparative genome database is the integration of genetic map and sequence data from two ACeDB-formatted genetic map databases: RiceGenes from Cornell University and SoyBase from Iowa State University. We present an integrated view of these two databases in graphical form and describe the process of transforming ACeDB data into the object-relational version of the commercially-available Oracle DBMS.