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 "hit").
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 MRC HGMP-RC Hinxton Cambridge CB10 1SB UK
From: "Brian Cox" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Subject: [Biojava-l] weightmatrix annotator Date: Wed, 26 Nov 2003 18:14:40 -0800
Hello,
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?
later, Brian Cox Samuel Lunenfeld Research Institute Mount Sinai Hospital, Rm 884 Toronto, Ontario Canada
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