Calculating Kn/Ks Per Site
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9.5 years ago
John ▴ 30

Hi all,

I've used PAML on an extensive multiple sequence alignment, running pairwise comparisons. I would also like to calculate strength of selection on individual sites. Is it possible with PAML or any other quickly executable programs?

Cheers,

Michael

selection evolution protein paml • 4.1k views
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9.5 years ago
Philippe ★ 1.9k

Hi Michael,

this is possible with PAML. You have to choose between different models: branch-specific model, site-specific model or branch-site model. They are all detailed in the PAML documentation. You can also check this online course for a more user friendly help. The PAML FAQ can also be of interest for some specific questions.

By the way, the common name for the ratio is either Ka/Ks or dN/dS, but not Kn/Ks.

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9.5 years ago
fransua ▴ 390

Hi, I am not sure you can find something about selective pressure by site doing pure pairwise analysis (runmode = -2), this is usually used for global distances. On the other hand doing site analysis you can get this info by site, but it is generally a bad idea to use this result when analyzing less than 4 sequences (if you try it, have a look to associated errors of the estimations).

have a look to this post: http://gsf.gc.ucdavis.edu/viewtopic.php?f=1&t=1099

an other program that can do this for you is SLR http://www.ebi.ac.uk/goldman/SLR/ but I am afraid that you will find same restrictions...

I think the best solution, if you can, is to group your sequences by 4.

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