thanks for your help Schiller, but I dont get how I can perform my various calculations on each sequence using your code. How can I push each extracted $dna into an array, which I can then iterate through for the calculations? This is the sort of thing I want to do for each sequence:

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

     my $token = $genome[$i] . $genome[$i+1];
     $freq{$token}++;
     $tt = $freq{tt};
     $cg = $freq{cg};
     $gc = $freq{gc};
     $ta = $freq{ta};
     $at = $freq{at};
     $cc = $freq{cc};
     $tg = $freq{tg};
     $ag = $freq{ag};
     $ac = $freq{ac};
     $ga = $freq{ga};
     $aa = $freq{aa};
     $gg = $freq{gg};
     $ca = $freq{ca};
     $ct = $freq{ct};
     $gt = $freq{gt};
     $tc = $freq{tc};

}
[download]

I have tried just using a simple 'push', but this slowed the program down far too much. cheers x

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