[Biojava-dev] RE: [Biojava-l] position weight matrix

[Schreiber, Mark]

Not wanting to argue but i'd love to hear why :)
 
- Mark
 

	-----Original Message----- 
	From: Matthew Pocock [mailto:matthew_pocock at yahoo.co.uk] 
	Sent: Thu 18/09/2003 9:14 p.m. 
	To: Schreiber, Mark 
	Cc: Brian Cox; biojava-l at biojava.org 
	Subject: Re: [Biojava-l] position weight matrix
	
	

	Schreiber, Mark wrote:
	
	>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
	> 
	>
	We should be taking the odds score between the weight matrix matching at
	that pos and the null model - that way, ambiguity symbols devide out.
	I'm tied up today (writing lectures - damn those students), but it
	should be easy to modify WeightMatrixAnnotator to accept a ScoreType
	instance.
	
	For reasons that we can argue about on -dev or off-line, you can't in
	the general case just divide scores for columns containing an N by 4, or
	portion them out relative to the null model. That's why the ScoreType
	objects were added to the DP package.
	
	Matthew
	
	>       -----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
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