Defining the edges of substitutional heterogeneity

Bob Friedman friedmar at
Wed Apr 11 11:07:31 EST 2001

The synonymous substitution rate should correspond to the underlying
mutation rate (see Kimura's work), so this rate shouldn't reveal protein
features.  With that said, in practice the synonymous rate does correlate
with changes in the nonsynonymous substitution rate, for whatever reason.
Added into the mix is synonymous codon usage in unicellular organisms versus
multicellular organisms where the former show bias for certain codons in a
gene that is transcribed in large amounts.
I imagine you can incorporate the above ideas into a model that then can be
used to predict exons, if that is your intent.  Otherwise, the tblastn tool
in the blast package, for instance, is powerful to detect genes when a
homolog is known; grailEXP and Genscan can be used to detect genes or exons
when homology is unknown.
Good luck,
Bob Friedman

"Guy Reeves" wrote in message > I am trying to ask the question, do the
edges of regions which show statistically different rates of synonymous
substitution coincide with genetic feature such as exon or gene boundaries?


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