[Bioperl-l] ortholog identification for many species

[Jason Stajich]

We don't solve this directly just yet but would ideally do this through a
definition of steps in the bioperl-pipeline as probably described by Elia.

For a sequence similarity approach to finding orthologues I would suggest
tools such as NCBI's COG and Sonnheimer group's InParanoid as examples of
automated orthologue detection.  InParanoid is still pairwise based but
one could imagine strategies starting from the set of pairwise findings.
http://www.cgr.ki.se/cgr/inparanoid/.  COG is more appropriate for
multiple species but I've never tried to get and run the software locally.

As for synteny based orthologue detection I don't believe there is a
formal framework in bioperl just yet but tools such as the Map objects
have been built so that implemeting the appropriate algorithm is easier.
This is definitely an area of active interest for a number of developers
but I don't think we've converged on an implementation that we all are
working on just yet.


-jason

On Fri, 5 Jul 2002, Martin Lercher wrote:

> 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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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu