[Bioperl-l] ortholog identification for many species

[Hilmar Lapp]

And 

Automated ortholog inference from phylogenetic trees and calculation of orthology reliability
Storm CE, Sonnhammer EL
Bioinformatics 2002 Jan;18(1):92-9
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=f1000&cmd=Retrieve&db=PubMed&list_uids=11836216&dopt=Abstract

may also be relevant (haven't read it yet) (it's cited and compared in Zmasek&Eddy). Jason, is this the Sonnhammer link you gave in a recent response?

	-hilmar

> -----Original Message-----
> From: Hilmar Lapp 
> Sent: Monday, July 08, 2002 10:30 AM
> To: Elia Stupka; Brian Osborne
> Cc: Martin Lercher; bioperl-l@bioperl.org
> Subject: RE: [Bioperl-l] ortholog identification for many species
> 
> 
> 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
> > 
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