NEW COMPUTATIONAL TOOLS FOR BRASSICA GENOME RESEARCH

¹ Plant Biotechnology Centre, Primary Industries Research Victoria, Department of Primary Industries, La Trobe University, Bundoora, Victoria 3086, Australia and Victorian Bioinformatics Consortium, Plant Biotechnology Centre, La Trobe University, Bundoora, Victoria 3086, Australia

² Plant Biotechnology Centre, Primary Industries Research Victoria, Department of Primary Industries, La Trobe University, Bundoora, Victoria 3086, Australia

³ Department of Biological Sciences, University of Bristol, Bristol, UK

With the ever increasing quantity of Brassica sequence and gene expression data, and in preparation for the complete genome sequencing effort, there is an growing requirement for the structuring of this information in a user friendly database. Towards this, we have developed an integrated Brassica database This database incorporates a sequence processing pipeline, followed by annotation against GenBank, SwissProt and Arabidopsis Gene Ontology (GO) data. All sequences are mined for SSR molecular markers using ‘SSR primer’ and e-mapped onto the complete Arabidopsis genome by sequence comparison. Planned extensions to this resource include the integration of gene expression data, the development of an EnsEMBL based viewer and a BAC end sequence mapping tool. The database may be queried using a text based search of sequence annotation or GO terms, BLAST comparison of resident sequences, or position of candidate orthologs within the Arabidopsis genome. The database is built using MySQL and perl, providing a high degree of platform flexibility and integration with external datasets, along with direct public internet access through a standard web browser.