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Question: (Closed) How To Compute Dn/Ds From Pairwise Alignment
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gravatar for gundalav
7.2 years ago by
gundalav • 300
La La Land
gundalav • 300 wrote:

I have a set of sequences (human 5'utr region), with which I already did pairwise alignment against chimp and rat whole genome. So I have the output in MAF and SAM format.

Is there any existing tool which can take these pairwise alignment and compute the dn/ds score?
alignment sequence evolution genomics • 2.7k views
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modified 7.2 years ago • written 7.2 years ago by gundalav • 300
6

Many very similar questions have been asked already, however your question doesn't make sense biologically. You have 5' UnTranslated Regions. There cannot be synonymous or non-synonymous substitutions in untranslated data!

Therefore I will close it. Please read http://en.wikipedia.org/wiki/Ka/Ks_ratio

ADD REPLY • link modified 7.2 years ago • written 7.2 years ago by Michael Dondrup ♦ 47k
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