Wednesday, August 26, 2009

Measuring recombination?

Whew! I've been slacking on the blog posts! Above: Probability of recombination between pairwise SNPs in a 15 strain alignment block of ~65 kb. Yellow indicates low probability of recombination...

The figure above was generated by PhiTest, a program that tries to identify regions of recombination between different taxa in a multiple alignment. Last night, I used MAUVE to generate a 15-way multiple alignment between the genome sequences of 15 different Haemophilus infleunzae isolates. (This took a while, but still was impressively quick.)

I grabbed a reasonably large alignment block (65,480 bp, including gaps) and stuck it into Phitest. It did everything reasonably quickly and gave me the unshocking result that there was a p = 0E+00 chance of no recombination occurring on the interval. So I decided to use the -g switch to provide a graphical output giving the chance of recombination between every pair-wise combination of SNPs (of which there were 9422; the program ignored indels).

This was fun, because it wrote such a gigantic file that my computer died due to lack of hard-drive space! That doesn't happen often! But it was mainly because I have several dozen gigabytes of stuff on my laptop that doesn't belong. I nudged a fraction of this aside and repeated the analysis to give the plot above.

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