[BiO BB] Is there a good way to find orthologue sequences?
sariego9 at yahoo.com
Fri Jun 17 16:04:01 EDT 2005
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)
--- "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.
> > 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.
> > _______________________________________________
> > Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> Bioinformatics.Org general forum - BiO_Bulletin_Board at bioinformatics.org
.=$=. .=$=. .=$=. .=$=. .=$=. .=$=.
@ @ | | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | |
| @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | |
| | @ | | | @ @ | | | @ | | | @ @ | | | @ | | | @ @ |
~' `~$~' `~$~' `~$~' `~$~' `~$~' `~
Find restaurants, movies, travel and more fun for the weekend. Check it out!
More information about the BBB