Some tools that will help:

• using split as: my @H1aAcids = split //, $H1 you get an array containing the individual letters (amino acids I presume)
• using a hash (see perldata) you can count the number of occurrences of each letter: $H1count{$_}++ for @H1aAcids

If you want any more help you're going to have to tell us in terms of a recipe (algorithm) how the output relates to the input or wait for one of the biologically knowledgeable monks to stroll by.