[Bioperl-l] Reciprocal blast

[Jay Hannah]

Dave Messina wrote:
> Your question is a little beyond the scope of this mailing list. I don't
> know what your bioinformatics background is, but in my experience it's best
> to get started hands-on, either in a class or with someone you can sit down
> and work through it with. You'll have a million questions, and a mailing
> list isn't really suitable for that.
>
> That being said, I would run the blasts on the command-line, parse out the
> best hits with BioPerl, and then use hashes to identify mutual best hits.
>   

Hi Matt,

If you're a glutton for punishment and want to see a ball of Perl that 
automates and tracks stats across my version of "reciprocal blasts" 
(mine is called cross_blast()), help yourself:

   svn checkout svn://vc.jays.net/seqlab seqlab

I abandoned my maiden voyage into bioinformatics, called "SeqLab," as a 
stand-alone entity when the subsequent thousand tasks I worked turned 
out to be unrelated to all the software I had built so far. My naive 
grand unification vision for all of bioinformatics didn't quite work out 
as I had planned. -laugh-  Nowadays I just cherry-pick solutions out of 
its guts on demand.  :)

I'm happy to field any questions you have about that code, if it helps 
you any.

Cheers,

j
http://clab.ist.unomaha.edu/CLAB/index.php/User:Jhannah