in reply to How do I find match patterns between two DNA sequences?

Here’s what I would suggest:

  1. Define your problem:   Before you can devise a computerized solution to a problem, you must define the problem exactly.
  2. Research “prior art”:   No matter what you are doing, it has been done before.   Review all the tutorials mentioned, books, whatever.   Carefully review the CPAN library to determine what resources you can use from there.
  3. Study regular-expressions:   “Regexes” are the basic Swiss Army Knife® for string-banging.   You will undoubtedly use them heavily in this application.