<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>With the increasing quantities of <italic>Brassica</italic> genomic data being entered into the
public domain and in preparation for the complete <italic>Brassica</italic> genome sequencing
effort, there is a growing requirement for the structuring and detailed bioinformatic
analysis of <italic>Brassica</italic> genomic information within a user-friendly database. At the Plant
Biotechnology Centre, Melbourne, Australia, we have developed a series of tools and
computational pipelines to assist in the processing and structuring of genomic data,
to aid its application to agricultural biotechnology research. These tools include a
sequence database, ASTRA, a sequence processing pipeline incorporating annotation
against GenBank, SwissProt and <italic>Arabidopsis</italic> Gene Ontology (GO) data and tools
for molecular marker discovery and comparative genome analysis. All sequences
are mined for simple sequence repeat (SSR) molecular markers using ‘SSR primer’
and mapped onto the complete <italic>Arabidopsis thaliana</italic> genome by sequence comparison.
The database may be queried using a text-based search of sequence annotation or GO
terms, BLAST comparison against resident sequences, or by the position of candidate
orthologues within the <italic>Arabidopsis</italic> genome. Tools have also been developed and
applied to the discovery of single nucleotide polymorphism (SNP) molecular markers
and the <italic>in silico</italic> mapping of <italic>Brassica</italic> BAC end sequences onto the <italic>Arabidopsis</italic>
genome. Planned extensions to this resource include the integration of gene expression
data and the development of an EnsEMBL-based genome viewer.</p>
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Comp Funct Genomics. 2004 Apr; 5(3):276-280