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

[yezhiqiang at gmail.com]

   Thank you all for these good suggestions and help for clear my
conceptions about ortholog and paralog.


2005/6/18, Marcos Oliveira de Carvalho <operon at cbiot.ufrgs.br>:
> 
> Another good discussion about orthology and paralogy can be found here:
> 
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12446146&dopt=Abstract
> 
> And Lerat et al, presents a novel approach for determining orthology in:
> 
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12975657&query_hl=4
> 
> Marcos
> 
> On Fri, 17 Jun 2005 17:04:01 -0300, Diego Martinez <sariego9 at yahoo.com>
> wrote:
> 
> > 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
> >>
> >>
> >>