hi monks, i have a string matching question. I want to be able to match complementary reversed sequences within an array. Certain letters are complements of each other e.g. A + T , C + G (in dna). I want to iterate through an array and match those strings that are complementary in the reverse orientation. e.g. GTTC + GAAC would be a match (GTTC complement is CAAG, which reversed is GAAC).

I am getting confused, do I need some sort of look-up table which says A -> T , C->G , G->C , T->A ?? If so, how can I do this?

Any help i'll be very grateful ;-> # below is my snippet of code, it is wrongly looking for exact matches, but I need to look for reverse complementary matches. 

for (my $i=0; $i < @array1; $i++)   {

    $dna = reverse $array1[$i];
    $dna =~ tr/actg/tgac/;

    if ($dna eq $array1[$i])   {

# problem is here, I am testing for equality, but need to test for com
+plementarity!

           print "\nFOUND $array1[$i] \t $dna";
    }
}

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In reply to string complement question by Anonymous Monk

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