in reply to Count Occurrences of a string

For your long-term benefit, one of a growing number of Perl books with bioinformatic slant, such as ISBN 0596000804, ISBN 0596003072, ISBN 052180177X, ISBN 1565926641 may be beneficial to you. (I am not qualified to comment on merit or demerit on any of these.)

A CPAN search on bioinformatics turns up a few modules, and might be of intereste to you.