IslandViewer

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!

Evaluation of genomic island predictors using a comparative genomics approach

Well after a long hiatus from blogging I thought would start again with announcing my recently accepted paper, "Evaluation of genomic island predictors using a comparative genomics approach" in BMC Bioinformatics.

Quick Summary
This research provides a comparison of several previously published tools that are used to predict genomic islands (large regions of HGT in bacteria).These tools use various methods of identifying abnormal sequence composition, such as GC percent, to predict regions of HGT. The predicitons made by these tools were compared to reference datasets of genomic islands (GIs) and non-GIs (very conserved regions) that were constructed using whole genome alignments. One of the novel and cool (well I like to think so) things about this comparative genomics method, called IslandPick, is that it automatically selects appropriate genomes for comparison given a query genome. Normally in most compartive genomics studies the user/scientist has to pick which genomes are relavant and should be used in the comparison. This works well until you have to do it for ~1000 different genomes. If you want more information on how this works read the paper!

Publishing
This was my first experience with a very tough and stubborn reviewer. This would have been published almost 6 months ago if it wasn't for one reviewer that kept insisting that our method was flawed even after we clearly defended and addressed their concerns. After much correspondence and waiting, a fresh group of reviewers accepted the research after some minor revisions. *Sigh* Makes me wonder how much of publishing is just a crapshoot?

Odd Ball Science

My summer was a busy one that included traveling to Germany, Austria, and England (not bad for my first trip to Europe), plus a trip home to New Brunswick/Nova Scotia. My blog took the greatest hit as I tried to keep up with my research and manuscript writing, but I hope to get back to regular blogging again.

I was one of the thousands at ISMB 2007 in Vienna, Austria and I was presenting a poster on research that I hope to submit to Bioinformatics in the next week or so. Basically, I study genomic islands (large regions of horizontal gene transfer) in bacteria including their identification, their evolutionary origins and their relationship with virulence.

During one of the poster sessions I entered a nice discussion with someone about my research. After about 30 minutes of explaining my methods, background details, future plans, etc. I asked the standard question, "What do you study and is it related to my research in anyway?" and his chipper response was "Oh, no I don't study anything like this. I just like going around to these posters on oddball topics." Now I can take suggestions, criticism, or even indifference, but "odd ball" made it feel like my research was irrelevant; leaving me to puzzle his comment for the next couple of days.

Anyway, after a visit with the bacterial annotation group at Sanger Centre, where people knew what genomic islands were and actually took some interest in my research I was worrying much less about my "odd ball " research.