[Bioperl-l] BLAST parsing Question
Thu, 9 May 2002 06:34:27 -0500 (CDT)
I encourage you to read the bioperl tutorial
The module to use is BPlite. For usage see:
On Wed, 8 May 2002, Simon K. Chan wrote:
> My fellow BioPerl-ers,
> It took me a couple of hours to realize that what I
> need to do is EXTREMELY common and that it's already
> been done. D'oh!! :-0
> So, I made a fasta database by using the formatdb
> command. I have a fasta file with a bunch of
> fasta file: seq A, seq B, seq C
> db made with formatdb: seq 1, seq 2, seq 3
> I blast the sequences in the file against the
> So, let's say that seq A only hits seq 1 with a P
> value of 10e-100 and seq B only hits seq 1 with a P
> value of 2e-15. Seq C hits nothing. How would I pull
> out that Seq A matches Seq1 and that Seq C AND Seq B
> match nothing?
> I tried to do this with hashes where the keys were the
> matches from the db and the values were arrays with
> the P value and query name. But it go real messy.
> Yuck! Does anyone know of a module or some other
> quick way of doing this?
> Thanks, all.
> Warmest Regards,
> Simon K. Chan - email@example.com
> "Great spirits have always encountered violent opposition from mediocre minds."
> - Albert Einstein
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