Were I autogenerating, my approach might be as follows (untested):

{
  my @c = qw(A T C G N);
  my @strings = @c;
  foreach (1..5) {
    foreach (@strings) {
      $sorted_str{$string} = join '', sort, split //;
    }
    @strings = map {
      my $string = $_;
      map $string.$_, @c;
    } @strings;
  }
}
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  $bases = $sorted{$bases}
    ||= join '', sort, split //, $bases;
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my @strings = (grep /[acgmt]{2}/, ('aa' .. 'tt'), 
               grep /[acgmt]{3}/, ('aaa' .. 'ttt'), 
               grep /[acgmt]{4}/, ('aaaa' .. 'tttt'));

my %sort_cache;

for my $key (@strings) {
    $sort_cache{$key} = join '',sort split('',$key);
}
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Guillaume,

I think one of the assumptions (although not clearly stated) is that no string has repeated characters in it.

Very inventive code though!

Update: Maybe a regexp to eliminate any string with duplicate letters. As though things weren't bad enough :)

If the code and the comments disagree, then both are probably wrong. -- Norm Schryer

length of 2: 5 . 4 = 20
length of 3: 5 . 4 . 3 = 60
length of 4: 5 . 4 . 3 . 2 = 120
total of 20 + 60 + 120 = 200 possibilities.

If the code and the comments disagree, then both are probably wrong. -- Norm Schryer