[BioC] sequence search using a position weight matrix?

[Paul Shannon]

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