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exons & protein domains

Gary DosSantos dossantos at paprican.ca
Tue Jul 23 17:07:09 EST 1996

> I think you should really focus on are individual structural domains.
> Structural domains of proteins are clearly 'modules' of evolution, and
> any given domain may have distant homologs in otherwise unrelated
> proteins.  Hence the unit of evolution is frequently no larger than
> the protein structural domain.  Furthermore, we have seen very few
> cases where regions of proteins smaller than a structural domain
> (include those which are exon-sized) are homologous in otherwise
> unrelated proteins.
> Protein structures have two crucial advantages over sequences.  First:
> you can look further back in history with them.  In some cases,
> similar protein structures may indicate a very distant evolutionary
> relationship between two proteins with insignificant sequence
> similarity.  Second: if proteins are of different structure, you can
> say with excellent confidence that they are unrelated.  By contrast,
> sequences which are dissimilar may have simply diverged too far to be
> recognizable.  So, structures allow you to identify distant
> relationships and to reject relationships as well.  Sequences can't.

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.

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