This might be overkill, but if regexes are feeling unwieldy or hard to maintain for your task, you might want to try it with a grammar and Parse::RecDescent.
in reply to Genbank file parsing
I haven't used P::RD myself yet, but am learning it because it seems like it would come in handy in a variety of situations where regexes won't quite get the job done, or get the job done kludgily. Also, perl 6 "rules" (the new word for the concept formerly known as regex) are shaping up to be sort of an amalgamation of regexes and formal grammar, with the formal grammar aspect closely related to the way grammar parsing works in P::RD. (Damian Conway, who did P::RD is also in charge of Perl 6 rules.)