[Bioperl-l] Re: Comparative genomics - regions of synteny and whole genome duplication

[Richard Copley]

 > You could get some clustering from large scale duplication
 > events before the species split.  Consider the 4 vertebrate
 > hox clusters.

Absolutely, but within species with 4 clusters, wouldn't you still expect the 
orthologous clusters to be more similar to each other than the paralogous 
clusters?

The only point I'm trying to make here is that conserved gene order reflects 
descent from a common ancestor (and not convergent evolution). So if you have 
a conserved block of genes in species A and the same block in species B, they 
are, by definition, orthologues. (Given that it contains enough genes to be 
statistically significant, and there is only one copy of the block per genome).

Now, reciprocal blast hits are a fine thing, and trees are a better thing, 
but I think if one has sufficiently closely related genomes, using gene order 
to define orthologues is worth investigating. If you're (Elia) unhappy about 
the blast aspect, you could look for conserved runs of PFAM domains, or 
Anton's families or something like that. Damn, I'd do it myself if I had time 
or another vertebrate genome to compare human to.


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  Richard Copley
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