I am indeed trying to read Fasta files.

In fact, what I'm doing is creating a search function that, given a variable number of user-input DNA sequences (such as amino acid motifs, or transcription factor binding sites), it searches a user specified Fasta file for all hits, either totally, or within $interval bases of each other, and then outputs all the hits both as .html format and as .fasta format, and the .html would have all the matches highlighted in various colors.

So far, I haven't read up at all on modules, so I suppose that's the next step in my Perl learning curve.

Thanks for the pointer. I'll definitely check it out.
Matt