[Biojava-l] Calculate mass and pI for a protein containingambiguity symbols

george waldon gwaldon at geneinfinity.org
Mon Apr 2 17:12:18 UTC 2007

Hi Susy,

As I am reading your mail, a fix is already implemented in the cvs for molecular weight calculation of polypeptides containing ambiguity symbols. I haven't done anything for pKs but I can get a look at this. Give me a few days.

George (not Bruce!)

-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Susy Griffiths
Sent: Monday, April 02, 2007 6:04 AM
To: biojava-l at lists.open-bio.org
Subject: [Biojava-l] Calculate mass and pI for a protein containingambiguity symbols

how can I avoid the IllegalSymbolException to calculate the mass and pI 
of a protein using BioJava, when the sequence contains 'X' or 'B'  or 'Z'?
The Expasy comput pI /Mw tool does this, see 
"In addition to the standard one-letter-codes for the 20 amino acids, 
the characters B, Z and X are accepted:

      B   Asx   Aspartic acid or Asparagine   
      Z   Glx   Glutamine or Glutamic acid
      X   Xaa   Any amino acid

The mass values used for these residues are mean values of the 
corresponding masses, and B, Z and X are presumed to have pK values of 
0, i.e. a pI of 5.52."

Would I need to edit the ResidueProperties.xml file to provide average 
mass entries for X, B & Z ?

thanks, Susy

Dr S.L. Griffiths
Department of Chemistry
University of York
YO10 5YW

email: susy at ysbl.york.ac.uk
Tel. +44 (0)1904 328270
Fax +44 (0)1904 328266

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