[BiO BB] Is there a good way to find orthologue sequences?

[Diego Martinez]

commonly the only way one will use the term
orthologous is if you are using all the genes
of 2 genomes.  The reasoning goes like this:
for gene A in genome 1, and for gene B in 
genome 2, if the highest scoring hit to gene A
from genome B is gene 2, and if the highest 
scoring hit to gene 2 from genome A is gene
1, then gene 1 and gene 2 are potential 
orthologs.  I hope I said that right.
This is called either bi-directional
best hits or mutual best hits.  It might
be easier to draw out also.  
Most researchers I know who deal with 
this sort of thing conclude that without the 
entire genome, you can not really
be sure that you are looking at a true 
ortholog, it could be a "co-ortholog"
or as Christoph said, a paralog.
Also see Overbeek et al (PNAS v.96(6); Mar 16, 1999)

Diego

--- "Dr. Christoph Gille" <christoph.gille at charite.de> wrote:

> There is always the danger of picking a paralogous sequence instead.
> If two genes are orthologous then the sequence identity should be
> typical for the two species.
> If they are paralogous the sequence identiy is higher.
> I am not convinced that this can be solved completely automatically.
> 
> Christoph
> 
> 
> 
> 
> > Dear all,
> > Is there a good way to find orthologue sequences? I mean, I have a
> > protein sequence in species A, how could I get all the available
> > corresponding sequences from other species?  I blast my sequence to nr,
> > there are just too many hits with low e-value and high identity, so that
> > some "corresponding" sequences from distant related species could not be
> > find by blast. Is there any good method for automatically solve this
> > problem?
> >
> > Thank you very much.
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> >
> 
> 
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