[Bioperl-l] Blast or blat against custom db?

[Sendu Bala]

Kevin Brown wrote:
[snip]
> So, my thought was to utilize something like blastall from within the
> script to find other oligos of similar match, but it means that I need
> to dump out the oligos designed, create the db with formatdb. [snip]
> I'm just trying to figure out how to do it all without leaving the
> script, but as yet haven't noticed a way to create a db from within perl
> using bioperl?
> 
> Any thoughts on directions I should look?

AFAIK there's no bioperl interface onto formatdb, but the way to do it 
is make a fasta file (perhaps using bioperl) with all the oligos (what 
you want to become the db), then use a perl system call (or similar) to 
run formatdb. Still in the same script you'd then run and analyse the 
blast with bioperl calls (presumably starting with StandAloneBlast - 
http://bioperl.org/wiki/HOWTO:Beginners#BLAST if you need it).

Just be sure to carefully craft your blast parameters so they're 
suitable for oligo-sized matches and test the 3' base of hits are identical.