AAFC Brassica / Arabidopsis Comparative Genome Viewer

Currently the main application of the Brassica / Arabidopsis Comparative Genome Browser (Browser) is to allow the visualization of the AAFC B. napus ESTs (3' and 5' sequences for 60,000 cDNAs) relative to the Arabidopsis genome sequence as annotated by TIGR.

Sequence data for the Arabidopsis thaliana genome was obtained from The Institute for Genomic Research website at http://www.tigr.org. Sequencing of the Arabidopsis thaliana genome was accomplished with support from the Arabidopsis Genome Initiative. We are currently using release 3.0 data.

The Browser allows visualization of Brassica DNA sequences relative to homologous sequences in the Arabidopsis genome. This visualization imparts on the B. napus sequence contextual information including: provisional physical mapping through conlinearity; access to the Arabidopsis gene annotation; and clustering of related members of Brassica multigene families.

• Brassica / Arabidopsis Comparative Genome Browser
• Note: The Brassica / Arabidopsis Comparative Genome Browser requires the SVG Plugin available from Adobe. Haven't got it? Download it here
• Users manual - PDF

To apply the AAFC Brassica / Arabidopsis Comparative Genome Viewer to visualize the relationships between B. napus ESTs and the Arabidopsis genome we determined the regions of similarity between the ESTs and the DNA sequence of the Arabidopsis pseudochromosomes using BLAST. This information was stored in a MySQL database, which allows the user to view all ESTs with similarity to any part of the Arabidopsis genome. The user can see how the different ESTs align with Arabidopsis genes, search for a specific gene or EST, access gene annotations, and identify duplicate genes in Arabidopsis. The viewer allows us to efficiently display similarities between a large number of ESTs over a large region of the Arabidopsis genome.

The Viewer is based on a Custom Graphical User Interface (CGUI) that has been implemented using SVG and Javascript to provide the client side front end to the Viewer. This same interface will facilitate the development of web based genome viewers for other genomes, and especially for the comparative analysis of model genomes with the genome of related organisms.

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