Try String::Approx should you not find what you want in anything specific to bioperl.

But this problem does not sound to me like a regex problem per se. I think you should back off from the code and explain your actual problem. For instance I suspect that something like the following untested code could be useful even though it sounds nothing like what you have written:

# Takes a string, returns hash of chars in string and
# how many times each appears.
sub char_count {
  my $str = shift;
  my %count;
  while ($str =~ /(.)/gs) {
    ++$count{$1};
  }
  return %count;
}
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