Plant & Animal Genomes XIII Conference Plant & Animal Genomes XIII ConferenceJanuary 15-19, 2005
Town & Country Convention Center
San Diego, CA
Recent advances, such as the availability of genome survey sequence data from Brassica oleracea and the advent of physical mapping projects, are radically transforming the means by which we can dissect Brassica genome structure and systematically relate it to that of Arabidopsis. Until now, our view of genome collinearity has been largely inferred from comparative RFLP data, necessitating substantial interpolation and expert interpretation. In the future, the Multinational Brassica Genome Project will enable an entirely computational approach to this problem. We have been developing databases and bioinformatics tools to support Brassica genomics and comparative genomics. Some of the work behind our recently completed draft physical map of B. rapa will be discussed, together with a project to integrate this with the A genome component of B. napus. We will also present new ways to display emerging Brassica-Arabidopsis sequence homology data. We have used the GMOD group’s Generic Genome Browser to map all publicly available Brassica sequences in the context of computed BLASTN similarity to the Arabidopsis TIGR v5 genome sequence. This in silico approach potentially identifies all paralogous sequences and so we colour-code the significance of the mappings and offer an integrated, real time multiple alignment tool to partition the candidate homologues into paralogous groups. Furthermore, the MySQL database driving the browser can also be directly interrogated using the powerful API offered by the Perl Bio::DB::GFF methods, facilitating a wide range of data-mining possibilities that will be illustrated. All these tools and data are publicly available at http://brassica.bbsrc.ac.uk/.