exons & protein domains

Wnn System Account wnn at evolution.genetics.washington.edu
Wed Jul 31 12:14:06 EST 1996

in an article that seems never to have reached me, (only Andrew Roger's reply)
Gary Dos Santos 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.

Am I missing something or is Dos Santos saying that we can only bootstrap
by sampling (or omitting) whole domains?  Why can't we boostrap by sampling
individual sites?

Joe Felsenstein         joe at genetics.washington.edu     (IP No.
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA

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