[Bioperl-l] BLAST parsing Question

Simon K. Chan bioinformatics_rocks@yahoo.com
Wed, 8 May 2002 18:45:23 -0700 (PDT)

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 - bioinformatics_rocks@yahoo.com

"Great spirits have always encountered violent opposition from mediocre minds."

- Albert Einstein

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