<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>Recent advances, such as the availability of extensive genome survey sequence (GSS)
data and draft physical maps, are radically transforming the means by which we
can dissect <italic>Brassica</italic> genome structure and systematically relate it to the <italic>Arabidopsis</italic>
model. Hitherto, our view of the co-linearities between these closely related genomes
had been largely inferred from comparative RFLP data, necessitating substantial
interpolation and expert interpretation. Sequencing of the <italic>Brassica rapa</italic> genome
by the Multinational <italic>Brassica</italic> Genome Project will, however, enable an entirely
computational approach to this problem. Meanwhile we have been developing
databases and bioinformatics tools to support our work in <italic>Brassica</italic> comparative
genomics, including a recently completed draft physical map of <italic>B. rapa</italic> integrated
with anchor probes derived from the <italic>Arabidopsis</italic> genome sequence. We are also
exploring new ways to display the emerging <italic>Brassica–Arabidopsis</italic> sequence homology
data. We have mapped all publicly available Brassica sequences <italic>in silico</italic> to the
<italic>Arabidopsis</italic> TIGR v5 genome sequence and published this in the ATIDB database
that uses Generic Genome Browser (GBrowse). This <italic>in silico</italic> 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 them
into paralogous groups. The MySQL database driving GBrowse 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.</p>
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Comp Funct Genomics. 2005 Apr; 6(3):147-152