[Bioperl-l] orthologous genes extracting
birney at ebi.ac.uk
Thu Aug 19 19:11:40 EDT 2004
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
> 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.
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