[Biojava-l] Protease and Digest classes

[Graeme Campbell]

Hi there,

I've been trying to create a list of peptides from a theoretical trypsin 
digest using BioJava.  I'm using the Protease and Digest classes, but 
for some reason there is no cleavage between R and Q residues (and 
possibly between K and Q), even though Protease.TRYPSIN is defined in 
ProteaseManager.xml as cleaving after R and K, but not before P. Here is 
the code I'm using:

Digest d = new Digest();
d.setMaxMissedCleavages(0);
Protease trypsin = Protease.getProteaseByName(Protease.TRYPSIN);
d.setProtese(trypsin);
d.setSequence(s);
try {
     d.addDigestFeatures();
}
catch (Exception e) {

}

When I attempt to create my own Protease with the same constraints 
(after K,R not before P) I get the same results.

Protease trypsin = new Protease("RK", true, "P");

However, if I create a protease with no cleavage exceptions it cleaves 
between R and Q.

Protease trypsin = new Protease("RK", true, "");

Can anyone tell me what is going wrong?

Thanks,

Graeme