sequence divergence puzzle

James McInerney, Zoology jamm at nhm.ac.uk
Sun Jan 31 12:05:40 EST 1999


Sam,

Is it possible that the nucleotide sequences are extremely biased in 
their base composition?  If you have two random DNA sequences composed of 
25% As 25% Ts etc.  Then you will have sequences of 25% similarity,simply by 
chance.  If the sequences are biased towards GC or AT, then the sequences 
will be closer to 50% similar, simply by chance.  This might be part of 
your problem.  Of course, this situation might be exacerbated by the fact 
that the sequences are not random, but they are related to each other at 
some level.

Of course, this is simply a guess.

Take care,

James

James O. McInerney,
Dept. of Zoology,
The Natural History Museum,
Cromwell road,
London SW7 5BD.
UK.




> I am not an evolutionary biologist but I am in the middle of writing
> my thesis and have a problem understanding this information. I have
> two sialidase genes from streptococcus pneumoniae which are more
> conserved at the nucleotide level (60%) than the amino acid level
> (53%). I thought this was usually the other way round.
> Ive checked the synonymous/nonsynonymous values using jukes-cantor 
> theyare 1.2+-0.25/0.46+-0.046.
>  Does anyone have any ideas? or other examples like this? 
> Sam king
> 
> 
> 
> 





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