[Bioperl-l] orthologous genes extracting

[Ewan Birney]

On Mon, 16 Aug 2004, Nathan (Nat) Goodman wrote:

> Paulo said:
> > I have been using Ensmart, Ensembl's web interface for batch retrieval,
> > at http://www.ensembl.org/Multi/martview
> > I think their orthologues are based on reciprocal BLASTs and sometimes
> > also on synteny and whole genome alignment data.
>
> Thanks.  I've seen problems with Ensembl similar to those with HomoloGene,
> but as I look through my notes, these may have been pathological cases.  For
> example, mouse Casp1 points to two human othologs, CASP1 and COP.  CASP1 is
> a biologically validated ortholog, but COP is pretty similar and adjacent to
> CASP1.
>
> I'm wondering if anyone has combined a curated data source, eg, MGD, with
> computed results to avoid cases like this.

We would like to do this Nat in the future, and looking into improving our
automated procedures as well.



>
> Looking at the bigger picture, I see a need for "orthology" maps at various
> levels of stringency.  What I'm discussing here is the most stringent case
> in which we try hard to assign 1 ortholog per species to each gene.  (I
> realize the issue is biologically complex and this simple notion will fail
> for biological reasons in many cases, which is why I'm hoping someone else
> has already solved the problem :)  It would be nice to also offer more
> permissive maps including ones based entirely on sequence similarity.
>
> Best,
> Nat
>
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