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

[Richard Copley]

Elia Stupka wrote:

> Some points in reply to Lukasz:
> 
> 
>>blocks of synteny are best defined by clusters of orthologue genes on
>>chromosomes.
>>
> 
> This is the strategy that I had outlined, which leaves us with the major
> question of assigning orthologues. Once orthologues are assigned
> correctly, one cand do "alignments" of chromosomes, as if they were
> sequences with similarities.


Well, do you actually need to define orthologues to do this? Doesn't the fact 
that you have a sufficient number of highly homologous linked genes in the 
same (or similar) order strongly point to the interpretation that they are 
orthologues (at least if you're doing a cross-species comparison)?




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  Richard Copley
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