[Biojava-l] Masked regions, X's, No Call's N's

[Kevin T. Pedretti]

Hello All,
  I'm just starting to use biojava and have already hit a roadblock.  The
DNA alphabet doesn't contain symbols for X's or N's so when I try to read
in a fasta sequence with these characters, it throws a bunch of
exceptions. Can I extend the alphabet to contain these characters and
expect everything else to still work.  Sorry if this has been covered
before and thanks for your help.

Kevin