silent/replacement mutation

Brian Foley btf at
Mon Apr 24 12:38:54 EST 2000

Frank Leithäuser wrote:
> Does anybody know how to score a mutation in terms of silent /
> replacement if there are two or even three mutations in a single codon?
> Is every mutation counted seperately as a replacement or silent mutation
> according to whether it would have caused an amino acid replacement and
> regardless of what the combined two or three mutations present in the
> codon would have resulted in?


for an explanation of how the PERL program
handles these cases.

here is part of that README file:

NOTE1: An example of how Sd and Sn is determined for a single 

Imagine you have TTA in one sequence, and CTT in the other. 
Two bases are different. TTA encodes Leu, as does CTT. If you
assume that the bases have changed one at a time, there are 
two paths: 

TTA (L) --> CTA (L) --> CTT (L) or
TTA (L) --> TTT (F) --> CTT (L). 

>From first path, count = .5syn + .5syn 
>From second path, count = .5nonsyn + .5nonsyn 
So this two base change would be 1 synonymous, 1 non-synonymous. 

> Thank you very much!
> Frank Leithaeuser
> ---

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