I think you are right Mary. I have vague memories of Ks being the number of
synonymous substitutions per synonymous site and Ka being the number of
non-syn. subs. per non-syn. site. These will be tend to be 1.0 each on
average when there is nothing funny happening.
dee dot higgins at you see see dot eye eee
"Mary K. Kuhner" <mkkuhner at kingman.genetics.washington.edu> wrote in message
news:90m5pa$2nt$1 at mercury.hgmp.mrc.ac.uk...
> In article <90luod$kkb$1 at mercury.hgmp.mrc.ac.uk>,
> James McInerney <james.o.mcinerney at may.ie> wrote:
>> >I have a question about selection on genes in HIV (but probably
> >In some HIV genes there is often a great excess of replacement
> >over silent substitutions. In the past we would say that this meant that
> >there was a positive selection event involved. However, if there is no
> >selective difference between substitutions that occur in synonymous and
> >non-synonymous sites then we would see about three times as many
> >substitutions that are replacement than silent.
>> I believe such studies generally take this into account. They reckon up
> how many sites *could* have a synonymous or nonsynonymous (S and N
> from here on) substitution, and weight by how many such substitutions
> could occur (a fourfold degenerate site contributes more possible
> S substitutions than a twofold ones). So the actual statistic is the
> ratio of "S mutations per S site" and "N mutations per N site". This is
> often said as "ratio of S to N" but it's actually more complicated.
>> I think the original paper on this was by Masatoshi Nei.
>> Hope this helps,
> Mary Kuhner mkkuhner at genetics.washington.edu>>> ---