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.
Des Higgins
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
anywhere).
> >In some HIV genes there is often a great excess of replacement
substitutions
> >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>>> ---
>>
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