Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

The Soybean Gbrowse Database Maps Relationships Between Soybean Genomic Features.

C Langin , J Shultz , N Lavu , D Wainer , J Iqbal , DA Lightfoot

  Genomics Core Facility, Southern. Illinois University, Carbondale, IL62901.USA. ga4082@siu,edu

Soybean genomic features form a complex web of associations. Clones, for example, can have relationships with loci, contigs, MTP’s, sequences, related genes, EST’s, QTL’s, BAC end matches, and other features, which likewise have relationships with additional features, which have further relationships, and so on. We developed an ontology to describe genomic relationships and created the Soybean GBrowse Database, a MySQL multi-table database, to store and query the information. We programmed Extropy, object-oriented Perl software, with heuristic algorithms to load the database, facilitate the manipulation of the data, and create GFF output, with numerous tracks, suitable for displaying results in the Genome Browser (GBrowse). This visual output greatly enables the further interpretation of the soybean genome. A CD ROM version of the database has beeen developed for use behind a firewall. The database homepage is at http://soybeangenome.siu.edu.
The project is open source and was supported by NSF project #9872635.