[Biojava-l] Variable modifications to Protein sequences

[Mark Schreiber]

Hi -
I think that the best approach would be to define your own custom
alphabet (possibly with a custom tokenization). You could then create
SymbolLists or sequences with this new alphabet.
- Mark

On 2/6/07, Salman Tahir <salmantahir1 at gmail.com> wrote:
> 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
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