[Biojava-l] Variable modifications to Protein sequences

[Salman Tahir]

Hi,

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
FLEKQNKER -> FLEKQNKER, FLEKhydroxo-BS2GD0QNKER, FLEKQNKhydroxo-BS2GD0ER,
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