[Bioperl-l] Parser for PSIBLAST -out_pssm ASN.1 PSSM

Fields, Christopher J cjfields at illinois.edu
Sat Mar 3 21:48:34 EST 2012

We do have a Bio::Matrix::IO::psiblast module in bioperl-live (and in past CPAN releases, of course) that seems to fit.  Of course that is from blastpgp, not BLAST+, so this assumes the format hasn't changed.


Bio::Matrix::PSM::IO - PSM parser


See Bio::Matrix::PSM::IO for documentation


Parser for ASCII matrices from PSI-BLAST (blastpgp program in
BLAST distribution).


On Mar 2, 2012, at 12:01 PM, William Pearson wrote:

> Can BioPerl (or Perl) parse the PSSM produced by BLAST+ psiblast with the -out_pssm command?
> FASTA parse the binary ASN.1, but not the ascii text version.
> Bill Pearson
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