[Biojava-l] weightmatrix annotator

Tanya Vavouri tvavouri at hotmail.com
Thu Nov 27 11:14:47 EST 2003

Hi Brian,

I have started using biojava to annotate sequences with weight matrices and 
have had the same problem. Basically, using the WeightMatrixAnnotator class 
I can annotate a sequence with multiple weight matrices, but the problem is 
that when I then look at the sequence features, I can't tell which feature 
corresponds to which weight matrix.

As a solution, I've modified the WeightMatrixAnnotator class so that the 
constructor can also take a String argument, which is the ID of my weight 
matrix and then the class saves that string as the Feature.type(instead of 

I also thought that it would be good for the WeightMatrixAnnotator to accept 
a database of Weight Matrices so that it can neatly annotate a sequence with 
many matrices.

Does anyone know if this can already be done with some other biojava classes 
or whether someone is already working on this ? If not, would it be worth me 
sending to biojava some classes that I've written to deal with these tasks ?

Tanya Vavouri

Graduate Student
Comparative Genomics Group
Cambridge CB10 1SB

>From: "Brian Cox" <cox at mshri.on.ca>
>To: <biojava-l at biojava.org>
>Subject: [Biojava-l] weightmatrix annotator
>Date: Wed, 26 Nov 2003 18:14:40 -0800
>Does the current method or is there a method that lets multiple weight 
>matrix annotations be on the same sequence.  I currently am annotating the 
>sequence then pulling the annotation off into a list then annotating with 
>the next matrix etc., is there a good way of iterating through all 
>matrices, annotating the sequence with out deleting the annotation previous 
>annotation? Perhaps it does this already and I did something wrong?
>Brian Cox
>Samuel Lunenfeld Research Institute
>Mount Sinai Hospital, Rm 884
>Toronto, Ontario
>Biojava-l mailing list  -  Biojava-l at biojava.org

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