It might be easier for you to use just strings rather than the overhead of arrays for this. Use the substr function to get the nth character in the sequence. 
my $dna1 = 'CACTATGAGTGATCGC';
my $dna2 = 'ACTGACTAATGCGTTG';

print "$dna1\n$dna2\n";

for (0 .. length($dna1)-1) {
    if (substr($dna1,$_,1) eq substr($dna2,$_,1)) {
        print ' ';
    } else {
        print '*';
    }
}
print "\n";

__END__
# prints this:

CACTATGAGTGATCGC
ACTGACTAATGCGTTG
**** ** *  *****

[download]
Also, there are quite a few problems in your original code. First, the value that you want to loop/iterate over is the number N when you are looking at the Nth character. But the foreach loop will set $base to each of the values in @lines1 and then to all the values in @lines2. You cannot get a pair of elements from two different arrays using a foreach loop. Also note that inside the loop, you are comparing the first elements of the array each time. You want to compare a different pair of elements each time through the loop. Lastly, @lines1[0] is invalid (at least until Perl6), and what you need to say instead is $lines1[0].

HTH and keep trying!

blokhead

In reply to Re: comparing strings by blokhead
in thread comparing strings by Anonymous Monk

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