exons & protein domains

Andrew J. Roger aroger at is.dal.ca
Mon Jul 29 12:37:28 EST 1996


Gary DosSantos wrote:
> 
> This is off the topic, but I was wondering if any algorithms have been
> written that allow for the generation of phylogenetic trees by aligning
> structural domains. A typical protein does not have all that many
> structural domains, certainly not enough to perform a bootstrap
> analysis. It seems to me then, that by using structural domains as a
> criteria for protein alignment, one could not obtain the amount of data
> necessary for estimating the degree of relatedness between groups of
> proteins, but could only say that such and such proteins are related.


Look in the last chapter of Methods in Enzymology, Volume 183. There
is a paper using three dimensional structure to construct
evolutionary trees (it is a distance method, I believe).

Cheers
Andrew Roger



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