Hi
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?
Ideally I would like a method that could find regions in a sequence with the most statistically different rates of synonymous substitution and then define as closely as possible their probable edges.
If possible I would like the method to be able to do this without a priori defining regions or window sizes (other than to specify a requirement for the regions to be greater than a particular value).
The method need not necessarily allow for phylogenetic structure as the 5kb protein fragments I am analyzing all radiate from a polytomy
Ideal or not I would be very interested in any approach along these lines
Thanks for any help
Guy
Guy Reeves
Smithsonian Tropical Research Institute
Naos Molecular Biology and Evolution Laboratory
Balboa
Republic of Panama
reevesg at naos.si.edu
telephone : 00507 212 8831 (direct)
Fax : 00507 212 8790
---
