[Bioperl-l] Generalized reciprocal blast

[Dave Messina]

Hi Robert,

Just to add another comment on this:

The problem of identifying orthologs is quite a bit trickier than it looks,
in part due to the many-to-many relationships you noted.

There is a whole body of literature on this topic -- here's a recent review
that includes OrthoMCL that Jason mentioned and others:

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000262

(disclaimer: I work in a lab that offers one of the many attempts to solve
this problem)

So I would say that although it is possible to make a customizable function
as you describe, there are several existing approaches (read: downloadable
code you can run on your data) that would probably give better results.


Dave