Question: MEGA6 and test for selective pressure
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gravatar for giulio.formenti
4.6 years ago by
Italy
giulio.formenti0 wrote:

Dear all,

I have been using MEGA6 for a while in order to evaluate some stats of my gene of interest.

One of the tests that is possible to conduct with MEGA6 is diversifyng/purifying selection. So here is the question. If I try to run the test with two divergent sequences on several exons of a gene I can find in many cases that puryfing selection is occurring (dS > dN significant). However, if I run the same test on an intronic sequence I also get a positive signal of purifying selection in many many (too many) cases. While there might be some selective pressure also acting on introns it is impossible that this is acting on a codon-like structure. I don't think that the issue is in the software so I guess there must be some flaw in my argument. However I don't see how a good statistical test could reject the null hypothesis if clearly random sequences (with respect to the test) are used.

Suggestions?

 

Thanks

alignment gene • 1.8k views
ADD COMMENTlink written 4.6 years ago by giulio.formenti0
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