Hi monks, I wondered if someone would be able to help me. I simply want to compare two strings of dna (complements of each other) and determine whether they are correctly matched. e.g given two strings 

ATCG..
TAGC..

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Compare the first position in each, second position etc...However, if a base in the string does'nt correspond to its correct complement in the second string i want to print out that base pair.(correct pairings are A-T and G-C) e.g. 

ACTG..
TGAT..

G-T is a mispair

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I thought about using substr but don't know how to use substr to compare two strings. Here is a snippet of what i've tried. Much thanks ;-) 
my @dna;  # contains the sequence
my @comp; # contains the complement


while (@dna)   {

    foreach my $base (@dna)   {

             ++$counter;

      }

   foreach my $base2 (@comp)   {

             ++$counter2;

      }

   if (($base[$counter] == 'A')  && ($base2[$counter2] !~ 'T')  {
  
              print "mismatch : $base[$counter] \t $base2[$counter2]\n
+";

     }

#  etc

}

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but obviuously using this approach i will have to type out the same line for each base in the sequence.

update (broquaint): title change (was newbie seeks help comparing strings)

In reply to need help comparing DNA compliments by Anonymous Monk

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