Please read. Thanks

Brian Foley btf at t10.lanl.gov
Tue Jan 28 13:56:07 EST 1997

Xia Xuhua wrote:
> Dear Colleagues,
> Attached is a short (657 words) article of mine that I 
> should appreciate your comments on. Thank you in advance.
> Xuhua Xia
>  Therefore, a nonsynonymous 
> substitution at the first or the third codon site is more
> nearly neutral and more likely fixed than a nonsynonymous
> substitution at the second codon site. This hypothesis 
> ...

	That was the first explanation that came to my mind 
also.  Leucine, isoleucine and valine all occur in the
codons with U in the second position.
	I suspect the your explanation accounts for almost
all of the difference between observed and expected mutation
rates at the 3 codon sites.  Other factors which might
influence the rate would be differences in transition/transversion
rates, differences in rates dinucleotide pairs (CpG mutates
frequently in mammals), and other biases.  I suspect these
would be negligible in most genes, but could influence the
rates calculated from a few genes.  
|Brian T. Foley                btf at t10.lanl.gov                      |
|HIV Database                  (505) 665-1970                        |
|Los Alamos National Lab       http://hiv-web.lanl.gov/index.html    |
|Los Alamos, NM 87544  U.S.A.  http://hiv-web.lanl.gov/~btf/home.html|

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