[Bioperl-l] PSI-BLAST Matrix Parser?

Stefan A Kirov skirov at utk.edu
Tue Sep 7 20:12:40 EDT 2004

I am not sure what object you are going to store your data in... Are you
going to develop your own class to hold the data or use an existing one?
Also is there any reason not to use Bio::AlignIO (it reads PSI-Blast as
far as I know)?

On Tue, 7 Sep 2004, James Thompson wrote:

>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
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org

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