Mmmm, my bad. I wasn't paying much attention (apparantly). I was still checking and printing the same stuff, which didn't really make sense. This should do the trick (still slow, and I'm looking forward to faster ways :) 
my $i;
my $j;
my $dna;
my $temp_dna;

for ($i=0; $i < @array1; $i++) {
   $dna = $array1[$i];
   $temp_dna = $dna;
   $dna = reverse $dna;
   $dna =~ tr/actg/tgac/;

   for ($j=0; $j < @array1; $j++) {
      if ($dna eq $array1[$j]) {
         print "FOUND $temp_dna\t$array[$j]\n";
      }
   }
}

[download]
Please note that I made a lot of steps to get to this. This could be shortened, but this is more readable (for me at least ;)
--
B10m

In reply to Re: string complement question by b10m
in thread string complement question by Anonymous Monk

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