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 <[EMAIL PROTECTED]> 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 > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
