[Bioperl-l] PSI-BLAST Matrix Parser?

James Thompson tex at biosysadmin.com
Tue Sep 7 01:06:12 EDT 2004

Dear Bioperl-ers,

I'd like to parse the output of a PSI-BLAST matrix, and I was wondering if
there was a Bioperl way of parsing these files. If not, I'd like to make my
code general enough to be committed, and I'd like some advice on where exactly
to put such a module. From my cursory knowledge of Bioperl, I think that adding
another format parser to Bio::Matrix::PSM::IO would be a good way to go.

I have a couple of questions:
- Does anyone know what the PSI-BLAST matrix format is called?
- Is this the correct place in which to put code for parsing this type of files?

The file format represents a position-specific scoring matrix with some added
statistical information, here's a general overview of the information available
from the matrix file:

Last position-specific scoring matrix computed, weighted observed percentages
rounded down, information per position, and relative weight of gapless real
matches to p seudocounts.

Any help is greatly appreciated.

James Thompson

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