[Biojava-l] Variable modifications to Protein sequences

Salman Tahir salmantahir1 at gmail.com
Tue Feb 6 11:21:41 UTC 2007


I am emailing regarding a java program that I am writing which deals with
the in silico manipulation of cross-linked peptides.

I would like to manipulate protein sequences by taking into account variable
modifications using BioJava classes (if possible). For example:

If I have the following variable modification:
hydroxo-BS2GD4 (N-term, K): 118.0563805

And the following sequence: FLEKQNKER (assuming it contains the N-term)

I need to generate the following sequences
FLEKhydroxo-BS2GD0QNKhydroxo-BS2GD0 ER, Fhydroxo-BS2GD0LEK QNKER and so on -
generating a total of 8 peptide sequences with different masses.

Is there a way i can generate these additional sequences using BioJava? Any
help would be mostly appreciated.

- Salman

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