[BioC] sequence search using a position weight matrix?

[Paul Gordon]

Hi Paul,

I don't think bioc does (though someone can correct me).  If you turn 
the pwm matrix 90 degrees clockwise,
you get a Position Specific Scoring Matrix (like a Gribskov profile, but 
without gap scores), which can be
matched to a string using the Viterbi algorithm.  There are ways to 
execute the Viterbi algorithm in R, see
for example:

http://tolstoy.newcastle.edu.au/R/help/06/03/23821.html

Regards,

Paul
> Does any bioc package support amino acid sequence search using a pre- 
> defined
> position weight matrix (pwm)?
>
> As best I can tell, Biostrings, for all of its capabilities, does not  
> support
> sequence matching using pwm's.  cosmo (again, as best I can tell)  
> does not
> accept a pwm as input; rather, it identifies pwm's from the input  
> sequences.
>
> I'd be delighted to find out I am wrong on one or both counts ... or  
> to hear
> of another bioc package that does sequence search with pwm's.
>
> For background:  I obtain position weight matrices which predict
> kinase substrates from Predikin (http://predikin.biosci.uq.edu.au/ 
> pkr/).  I wish
> to use these matrices to search for possible kinase substrates in  
> peptide sequences
> obtained from mass spectrometry.
>
> Many thanks --
>
>   - Paul
>
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