[Bioperl-l] ortholog identification for many species

[Hilmar Lapp]

This doesn't solve all that you want I believe, but you may want to check it nevertheless:

RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs
Christian M Zmasek  and Sean R Eddy 
http://www.biomedcentral.com/1471-2105/3/14/

	-hilmar

> -----Original Message-----
> From: Elia Stupka [mailto:elia@fugu-sg.org]
> Sent: Sunday, July 07, 2002 10:41 PM
> To: Brian Osborne
> Cc: Martin Lercher; bioperl-l@bioperl.org
> Subject: RE: [Bioperl-l] ortholog identification for many species
> 
> 
> > Some would argue, and I've heard it argued, that orthologs 
> are those pairs
> > of genes that have arisen from a single gene in the 
> ancestral genome. What
> 
> We've had major debates over this definition already, so I'd 
> rather focus
> on practical aspects of it. I think right now some of the 
> most promising
> methods that would span multiple organisms would be related to
> phylogenetic trees. What I think many of us including Jason and me are
> hoping to achieve at some point is a complex and integrated enough
> represenation of proteins, their phylogenetic trees and other 
> properties
> to try to build automated methods for orthologue finding 
> based on the tree
> topologies.
> 
> The other approach is somewhat more simplistic, but in no way 
> should be
> discarded, and that is to decide what you consider a good orthologue
> finding method for a pair of organisms depending on your 
> strictness (from
> reciprocal best blast, to ensembl's seeds and pips, to Wolfe's
> methodology) and apply to many organisms pairwise. This will 
> definitely
> prove to be more accurate as once you put in multiple genomes you are
> bound to make arbitrary decisions about what is in what is 
> out, what is
> a paralogue,etc. As more genomes are completed and thus the average
> evolutionary distance between sequenced genomes gets smaller 
> this should
> also be a feasible and clean approach.
> 
> Elia
> 
> ********************************
> * http://www.fugu-sg.org/~elia *
> * tel:    +65 6874 1467        *
> * mobile: +65 9030 7613        *
> * fax:    +65 6777 0402        *
> ********************************
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>