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
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