Plant & Animal Genomes XIII Conference Plant & Animal Genomes XIII ConferenceJanuary 15-19, 2005
Town & Country Convention Center
San Diego, CA
C Langin , J Shultz , N Lavu , D Wainer , J Iqbal , DA Lightfoot
Genomic features form a complex web of associations. Clones, for example, can have relationships with loci, contigs, Minimum Tiling Paths (MTP’s), sequences, related genes, Expressed Sequence Tags (EST’s), Quantitative Trait Loci (QTL’s), Bacterial Artificial Clone (BAC) end matches, and other features, which likewise have relationships with additional features, which have further relationships, and so on. We needed methods to describe, store, manipulate, retrieve, and display these relationships. Results: We developed an ontology to describe genomic relationships and created an SQL 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 education, discovery, the generation of hypotheses, and the motivation of new methods for data analysis concerning the soybean genome. Availability: . A C-map version was developed at SIUC and runs on the same machine as Gbrowse. The GFF file was transferred to NCGR for use in their LIS system. We found the transfer of data was trouble free and provided valuable extra security. The three SIUC machines were hacked into on September 23, 2004. The resulting damage took 14 days to repair (estimated). In that time the representation at NCGR was the only form available to the community. The NCGR database can be interactively accessed at http://xgiprev.ncgr.org. All data, source code, and the GBrowse display are available at http://soybeangenome.siu.edu. NSF #9872635