only few words to add: i think all bioinformatic (due to the biggness of their data) need to learn a new word/concept: Iterator.
High Order Perl has a wonderful chapter about and in CPAN there is an implementation module: Iterator.
hth L*
There are no rules, there are no thumbs..
Reinvent the wheel, then learn The Wheel; may be one day you reinvent one of THE WHEELS.