I hadn't considered the Needleman-Wunsch because I forgot it was in BioPerl. I cobble scripts for minor text manipulations and haven't looked at too many modules including BioPerl. Being a biologist I really should give it a look.

On the other hand, I must say, it has been fascinating to read all the responses. The posting perlmonks have brought a lot to my plate, and I'll be reading and re-reading the posts for some time. My near non-existant skills can only improve because of their discussions.

Thanks for the tip. I'll read through the documentation for Bio::Tools::dpAlign.

I've looked at the Needleman-Wunsch information and I can probably get what I want by using high gap, gap extention, and mismatch penalties. The problem I see is that I can't specify a lower limit for the length of the match string found by Needleman-Wunsch.