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Assessing statistical sig. of difference in dn/ds (Read 1340 times)

Matt

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Assessing statistical sig. of difference in dn/ds
Apr 28^th, 2010 at 11:47am

Hello,

I have sequenced some MHC genes from 2 species of rodents, and want to know if selection is acting with greater intensity on one of the 2. I have about 50 individuals from each species.

I have generated estimates of omega for each species REL, FEL, SLAC, iFEL. So, for each species, I have 4 independent estimates of omega. To the eye, there is a difference in the predicted direction, but obviously I want to place a p-value on this difference. This is the question- how to evaluate the difference.

I am wondering if I can safely use the CompareSelectivePressure.bf, which was intended for populations...

Is there a better way to go about testing for differences in omega between 2 different species? Maybe some sort of bootstrapping procedure?

Thanks. Matt

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Sergei

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Re: Assessing statistical sig. of difference in dn/ds
Reply #1 - Apr 30^th, 2010 at 7:31am

Hi Matt,

If anything, CompareSelectivePressure.bf is more suitable for a between-species comparison, which is the traditional domain of omega-based analyses.

You can use that file to decide if there is evidence for more sites with omega>1 in one of the alignments, or if the value of omega is greater in one or the other.

It is definitely possible to bootstrap the p-value from CompareSelectivePressure.bf, but fundamentally, it is the same test: do two rate distributions differ or not.

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