[BioC] sequence search using a position weight matrix?

[Herve Pages]

Hi Paul,

No there is no support for PWMs in Biostrings. To deal with ambiguities
there is support for the use of extended IUPAC letters in the pattern (see
the 'fixed' arg in ?matchPattern) but unfortunately this is for a pattern
of nucleotides, not for amino acids.

Cheers,
H.

Paul Shannon wrote:
> 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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