[Bioperl-l] determining orthologs...

Ewan Birney birney at ebi.ac.uk
Tue Mar 16 04:07:10 EST 2004

On Mon, 15 Mar 2004, Bob Freeman wrote:

> What are BioPerl developers doing at present to determine putative
> orthologs of a gene? BLINK? Unigene? LocusLink? And what about for
> new/hypothetical genes?

Just to mention Bob, Ensembl, which is not a Bioperl thing per-se,
calculates orthologs across its clades (eg, all vertebrates) which
includes a dn/ds estimation for close species (eg, inter-mammal) from
PAML, where you can get out dn, ds, k (that's Kappa, not K :)) etc from
the database.

This is all accessible in the underlying databases and in the Mart data
mining tool (go to Ensembl --> Human --> Data mining and have a play...)

> Tx,
> Bob
> --
> -----------------------------------------------------
> Bob Freeman, Ph.D.
> Acorn Worm Informatics
> Dept of Systems Biology, C1-514A
> Harvard Medical School
> 240 Longwood Avenue
> Boston, MA  02115
> 617/699.7057, vox
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