Hi monks, My problem is that given a DNA sequence is am trying to find all the pairs in it e.g. ATACG = AT TA AC CG. I have written a sub-routine that handles this fine. I am trying to extend the sub-routine so it calculates the frequency of each pair and sorts the pairs accordingly. However, what I have written makes no change to the output. Please could you try to point out my mistakes?! Any help is massively appreciated. 
# snippet

@pairs = get_nn_pairs (@segment1);




sub get_nn_pairs    {


          (@segment1) = @_;
          my $base;
          my $pair;
          my @pairs;
          my $i;
          my $nn_pair;



          #  find and print all nn pairs form the sequence.



          foreach $i (1..$#segment1)      {


               $base = $segment1[$i-1];
               $pair = $segment1[$i];
               @pairs = "$segment1[$i-1]$segment1[$i]\n";


# only seems to know the value of @pairs from inside foreach loop


        # problems start here.

        @pairs = split ('', $nn_pair);

         my %freq;

         foreach  $nn_pair (@pairs)    {

                 {$freq{$_}++}

         }

  my @sorted_array = sort { $freq{$b} <=> $freq{$a} } keys %freq;

         print @sorted_array;

      }

   }

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In reply to subroutine problem by Anonymous Monk

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