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

Richard Copley copley@embl-heidelberg.de
Wed, 03 Oct 2001 14:27:17 +0200

Elia Stupka wrote:

> Some points in reply to Lukasz:
>>blocks of synteny are best defined by clusters of orthologue genes on
> 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)?

  Richard Copley
  69012 Heidelberg
  Tel: +49 6221 387 534
  FAX: +49 6221 387 517