The index functions is also your friend, see the relevant perldoc.

However, for serious work (i.e. long strings) you may want to have a look at the following book:

@BOOK{Gusf97,
  title = {Algorithms on strings, trees and sequences},
  publisher = {Cambridge University Press},
  year = {1997},
  author = {Dan Gusfield},
  address = {Cambridge},
}

or the BioPerl project.

Hope this helps, -gjb-