@nucleotides=('A','T','G','C');
foreach(1..1000)
    {
    $seq1.=$nucleotides[int(rand(3))];
    }
foreach(1..1000)
    {
    $seq2.=$nucleotides[int(rand(3))];
    }

[download]

You are only using the first three elements of the array @nucleotides.    The proper way to do that is: 

my @nucleotides = qw( A T G C );
foreach ( 1 .. 1_000 )
    {
    $seq1 .= $nucleotides[ rand @nucleotides ];
    $seq2 .= $nucleotides[ rand @nucleotides ];
    }

[download]


@seq1=split('',$seq1);
foreach(1..$window_size)
    {
    shift@seq1;
    }
@seq2=split('',$seq2);
foreach(1..$window_size)
    {
    shift@seq2;
    }

[download]

The usual way to do that is: 

my @seq1 = split //, $seq1;
splice @seq1, 0, $window_size;
my @seq2 = split //, $seq2;
splice @seq2, 0, $window_size;

[download]


open(OUT,">ID_matrix.txt");

[download]

You should always verify that open worked correctly: 

open OUT, '>', 'ID_matrix.txt' or die "Cannot open 'ID_matrix.txt' bec
+ause: $!";

[download]

In reply to Re: Speed up DNA dotplot by jwkrahn
in thread Speed up DNA dotplot by Microcebus

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