Late to the party, again, but one thing nobody has commented on is that your if-structure re-tests the same thing multiple times. Instead of: 
if (($genome[$i] eq 'a') && ($genome[$i+1] eq 'a'))    { ++$tt; }
         elsif (($genome[$i] eq 'a') && ($genome[$i+1] eq 'g')) { ++$a
+g; }
         elsif (($genome[$i] eq 'a') && ($genome[$i+1] eq 'c')) { ++$a
+c; }
         elsif (($genome[$i] eq 'a') && ($genome[$i+1] eq 't')) { ++$a
+t; }
         elsif (($genome[$i] eq 't') && ($genome[$i+1] eq 'a')) { ++$t
+a; }
         elsif (($genome[$i] eq 't') && ($genome[$i+1] eq 'g')) { ++$t
+g; }
         elsif (($genome[$i] eq 't') && ($genome[$i+1] eq 'c')) { ++$g
+a; }
         elsif (($genome[$i] eq 't') && ($genome[$i+1] eq 't')) { ++$t
+t; }

[download]
you should have had: 
if ($genome[$i] eq 'a') {
    if    ($genome[$i+1] eq 'a') { ++$tt; }
    elsif ($genome[$i+1] eq 'g') { ++$ag; }
    elsif ($genome[$i+1] eq 'c') { ++$ac; }
    elsif ($genome[$i+1] eq 't') { ++$at; }
}
elsif ($genome[$i] eq 't') {
    if    ($genome[$i+1] eq 'a') { ++$ta; }
    elsif ($genome[$i+1] eq 'g') { ++$tg; }
    elsif ($genome[$i+1] eq 'c') { ++$ga; }
    elsif ($genome[$i+1] eq 't') { ++$tt; }

[download]
etc.

Of course, the hash is a better solution for this problem, but I thought that the redundant testing problem should be pointed out.

In reply to Re: how can I speed up this perl?? by Roy Johnson
in thread how can I speed up this perl?? by Anonymous Monk

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