Hi, I have issues designing a code that scans 2 DNA sequences (taken as input from user, of same length) and then compares the two sequences, nucleotide by nucleotide (e.g. compare nt 1 from sequence 1, with nt 1 from sequence 2 etc). I'm new to perl, I've tried several different ways but I don't seem to get anything working. With the code that I've tried, nothing is printed out at all, so the nested foreach loops seem to get stuck somewhere. I would be greatful for some help/advice. PS I know I should use script, I deleted all that to simplify my problem and will add all that later on once I figured out this problem. Code: 
#!/usr/bin/perl
use warnings;


print("Please enter the first DNA sequence: ");
$DNAsequence1 = <STDIN>;
chomp($DNAsequence1);                                                 
+           
$DNAsequence1=uc($DNAsequence1);    
 $lengthDNA1=length $DNAsequence1;

print("\nPlease enter the second DNA sequenc (of same length as the fi
+rst): ");
$DNAsequence2 = <STDIN>;
chomp($DNAsequence2);                                                 
+           
$DNAsequence2=uc($DNAsequence2);
$lengthDNA2=length $DNAsequence2;
#print "The length of DNA sequence 2 is $lengthDNA2";

    if ($lengthDNA1==$lengthDNA2){    
print "DNA sequence 1: $DNAsequence1\nDNA sequence 2: $DNAsequence2\n"
+;
} else {
    print "\nThe DNA sequences are not of same lenght, please  try aga
+in!";
}

 @DNAsequence1=split(//,$DNAsequence1);
 @DNAsequence2=split(//,$DNAsequence2);


$score=0;                                 


foreach $base1 (@$DNAsequence1)
print $score;
{
    foreach $base2(@$DNAsequence2)
    {
        if($base1->[0] eq $base2->[0])
        {
    $score += 3;
    print $score;
} else 
{
    $score=$score+1; 
    }
}
}
print $score;

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In reply to nested foreach loop, match DNA sequences and calculate score by NadjaPadjala

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