Thanks to all of you for helping me out with this!
I'm a little embarrassed that I didn't check my thread before now...but I was trapped into doing other things grant related (have to pay the bills somehow).

Anyway, now I can hopefully get back to the more fun stuff, which is of course writing Perl scripts. :)

I will implement your various suggestions and see which one works the best and can handle some of the more complicated data that I will need to analyze. I just wanted to post something right away to let you all know how grateful I am for the amazing suggestions - you guys are awesome.

I'll post something later to let you know how it all goes.

By the way, nice job calling them genes Beth, I was wondering if anyone would notice. ;)

-Mat