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?
modified 7.6 years ago
•
written
7.6 years ago by
gundalav • 310
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!
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