[Biojava-l] position weight matrix

[Schreiber, Mark]

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:cox at mshri.on.ca] 
	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; biojava-l at biojava.org
	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: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
	=======================================================================
	Attention: The information contained in this message and/or attachments
	from AgResearch Limited is intended only for the persons or entities
	to which it is addressed and may contain confidential and/or privileged
	material. Any review, retransmission, dissemination or other use of, or
	taking of any action in reliance upon, this information by persons or
	entities other than the intended recipients is prohibited by AgResearch
	Limited. If you have received this message in error, please notify the
	sender immediately.
	=======================================================================
	


=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================