[Biojava-l] BioJava for SNP analysis?

[Rick Byers]

Hi,
I'm writing some Java code for analyzing SNP microarray data.  I'd like to
move to an open-source framework so I can leverage a community.  To what
extent is BioJava appropriate for SNP analysis?  I don't see any code,
documentation or samples that use microarray data (although I do see it
listed as a potential 'other' module for BioJava 3).  Is it reasonable to
just use a Sequence for all the data points and define features for each
SNP?  Or is there really nothing I'd want to re-use from BioJava beyond the
basic DNA alphabet?

If BioJava isn't a great framework to use for SNP microarray analysis, does
anyone know of an open-source project (preferably Java) that is?

Thanks!
   Rick