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

Susy Griffiths susy at ysbl.york.ac.uk
Mon Apr 2 13:04:26 UTC 2007

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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