[Bioperl-l] ortholog identification for many species

[Hilmar Lapp]

Have you checked NCBI's COGs (Clusters of Orthologous Genes)?

	-hilmar

> -----Original Message-----
> From: Martin Lercher [mailto:m.j.lercher@bath.ac.uk]
> Sent: Friday, July 05, 2002 3:29 AM
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] ortholog identification for many species
> 
> 
> Hi,
> 
> I have to identify a large number of orthologs for a dozen or 
> so species.
> There was a discussion on the identification of orthologs 
> here some months
> ago (and  I got some information from Elia on the approach 
> they took for the
> Fugu project); however, my impression is that the methods 
> discussed there
> were more useful for a 2-species problem.
> 
> My feeling is that to identify orthologs in many species, one 
> has to draw a
> phylogenetic tree for all homologous sequences, and look for 
> clusters of
> genes that contain exactly one gene for each species (or, if 
> more than one
> gene for one species, these should be clustered together). 
> Has anything
> similar to this approach been implemented in Bioperl (or at 
> all)? Or would
> you suggest a different approach?
> 
> Cheers,
> Martin
> ________________________
> 
> Martin Lercher, Ph.D.
> Department of Biology and Biochemistry
> University of Bath
> Claverton Down
> Bath,  Somerset
> BA2 7AY, UK
> Tel. +49-178-2573652
> Fax +44-1225-386779
> email: m.j.lercher@bath.ac.uk
> 
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