To ikegami, Roy Johnson, Pustular Postulant, graff, and frodo72:

Thanks for the advice; I started with graff's (it worked well) and will be digesting the rest of the replies this weekend.

frodo72: I know the module is somewhat rough-hewn, not to mention untested -- I wish I could find one that was more polished. It totally amazes me that it was a SWIG translation and it works... but it does!

The beauty of a suffix tree is that it gives the whole spectrum of repeated subsequences very quickly. So it (with Perl) is powerful at extracting data from dna from persons with Huntington's Disease or hereditary non-polyposis colon cancer and several other diseases where the defect may be a repeated (CAG)*n or another short, repeated theme.

Thanks, all, again for the help.

fdillon