[Biojava-l] Xs in DNA Alphabet

[David Waring]

I read in the archives that the issue of adding x to the DNA Alphabet came
up about a year ago. I have added it to my local version of biojava without
difficulty.

There are programs out there that use x as well as n, so we do come across
it in files generated by these programs. phrap and cross_match for example
treat x and n differently. X being having a negative match score and N
having 0. This allows using X as a way of masking sequences that you do not
want to match.

I wonder what other people think about putting this into the biojava
release.

David

|||||||||||||||||||||||||||||||||||||||||||||||||||||||
|   David Waring
|   Systems Programmer
|   University of Washington Genome Center
|   dwaring@u.washington.edu
|   (206) 221-6902
|||||||||||||||||||||||||||||||||||||||||||||||||||||||