Hello people, I've been using biojava for a few weeks now, and I've found a couple of problems with the proteomics tools.
First, org.biojava.bio.proteomics.MassCalc gives me inaccurate masses for the peptides. I noticed that the masses given by the Expasy mass calculator were a bit smaller for the peptides. Looking at the code I think I found out why: The code adds two times the mass of the OH group, whereas it should be added only once for the C-terminal, since the N-terminal gains an H, NOT an OH. Additionally, if the boolean MH_PLUS is set to true, a third OH is added instead of an (H+). Second, I've found that if I create more than one protease, when trying to digest a sequence the last created protease will be used, regardless of which one was specified with digest.setProtese(). So, if I want to use more than one (like digest with CnBR, grab the fragments longer than X, digest them with trypsin), I have to define it just before the digest, so I have to store the parameters for that protease somewhere else. Or am I missing something? Cheers, Roger Moraga. __________________________________________________ Do You Yahoo!? Yahoo! Tax Center - online filing with TurboTax http://taxes.yahoo.com/ _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
