[Biojava-l] position weight matrix

[Schreiber, Mark]

Hi Brian,

Technically this is correct as N or X do actually match everything. Are wanting to rule out any motif with an N or are you wanting to penalize a motif with an N (or other ambiguity)?

If you are working with DNA you could use org.biojava.bio.seq.NucleotideTools, this class can be used to access the nucleotide alphabet that treats all symbols as Atomic, even if they are normally IUPAC ambiguity symbols. If you did this and set the weight of N in the marix to 0.0 it would exclude those motifs.

- Mark



-----Original Message-----
From: Brian Cox [mailto:cox at mshri.on.ca] 
Sent: Friday, 12 September 2003 11:07 a.m.
To: biojava-l at biojava.org
Subject: [Biojava-l] position weight matrix


I wrote a program to find TF binding sites using a WeightMatrixAnnotator, but when I try to annotate a sequence if the sequences has any N or X then everything matches.  How do I get the WeightMatrixAnnotator to ignore the Ns or Xs?
thanks,
Brian Cox
Samuel Lunenfeld Research Institute
Mount Sinai Hospital, Rm 884
Toronto, Ontario
Canada

416-586-8266
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