Tuesday, November 18, 2008


My most recent research has resulted in website for viewing predictions of genomic islands (GIs), large regions of horizontal gene transfer, in bacterial genomes. IslandViewer integrates three different methods of GI detection IslandPick, SIGI-HMM, and IslandPath-DIMOB. SIGI-HMM and IslandPath-DIMOB use sequence composition bias to detect GIs and were found to be the most accurate in a recent publication. IslandPick is a method I recently developed that uses comparative genomics to find GIs by identifying regions that are present in one genome but absent from several related genomes.

Predictions for all three tools are pre-computed for all sequenced bacterial genomes (those available from NCBI Microbial genomes). Also, users can submit their own newly sequenced genome for analysis and receive an email when complete (usually within a couple of hours).

Update:IslandViewer has been published in Bioinformatics!

Any feedback or comments on the design or usefulness on the website is appreciated!


Pierre Lindenbaum said...

just a suggestion: use embedded SVG to draw your image and add meta-information (rdf) in it.

Morgan Langille said...

Pierre, thanks for the suggestion! When I started developing the site I looked into using SVG, since it would allow easy resizing of the image. However, I gave up on it after a few tests, since different browsers were having problems rendering it. In addition, I am a beginner with using SVG and googling for good tutorials wasn't very successful. Maybe I will revisit it in the future.