Brian,
I think we should change WeightMatrix so that N only scores a quater match of A where
as R would score a half match.
Do others feel this is sensible?
- Mark
-----Original Message-----
From: Brian Cox [mailto:[EMAIL PROTECTED]
Sent: Thu 18/09/2003 2:35 p.m.
To: Schreiber, Mark
Cc:
Subject: RE: [Biojava-l] position weight matrix
Thanks,
That sounds like what I was looking for, I wanted to penalize the use of an
N in the sequence. Not sure yet how to implement this but I'll give it a
shot.
thanks for the reply,
BRian
-----Original Message-----
From: Schreiber, Mark
To: Brian Cox; [EMAIL PROTECTED]
Sent: 9/17/03 7:45 PM
Subject: RE: [Biojava-l] position weight matrix
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:[EMAIL PROTECTED]
Sent: Friday, 12 September 2003 11:07 a.m.
To: [EMAIL PROTECTED]
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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