HIV mutation question

Mary K.Kuhner mkkuhner at kingman.genetics.washington.edu
Wed Dec 6 13:42:41 EST 2000

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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