Dear monks, I have written a script that operates on long sequences (e.g. 3 million characters).

The program is far slower than expected and I need it to be a lot quicker. I used the Benchmark module to determine which part of the code was being soo slow and it turned out to be this bit below;

Does anyone know of a way to speed this bit of code up? It is just calculating frequencies of different base pairs in a sequence. Cheers! 

 if (($genome[$i] eq 'a') && ($genome[$i+1] eq 'a'))    { ++$tt; }
          elsif (($genome[$i] eq 'a') && ($genome[$i+1] eq 'g')) { ++$
+ag; }
          elsif (($genome[$i] eq 'a') && ($genome[$i+1] eq 'c')) { ++$
+ac; }
          elsif (($genome[$i] eq 'a') && ($genome[$i+1] eq 't')) { ++$
+at; }
          elsif (($genome[$i] eq 't') && ($genome[$i+1] eq 'a')) { ++$
+ta; }
          elsif (($genome[$i] eq 't') && ($genome[$i+1] eq 'g')) { ++$
+tg; }
          elsif (($genome[$i] eq 't') && ($genome[$i+1] eq 'c')) { ++$
+ga; }
          elsif (($genome[$i] eq 't') && ($genome[$i+1] eq 't')) { ++$
+tt; }
          elsif (($genome[$i] eq 'c') && ($genome[$i+1] eq 'a')) { ++$
+tg; }
          elsif (($genome[$i] eq 'c') && ($genome[$i+1] eq 'g')) { ++$
+cg; }
          elsif (($genome[$i] eq 'c') && ($genome[$i+1] eq 'c')) { ++$
+cc; }
          elsif (($genome[$i] eq 'c') && ($genome[$i+1] eq 't')) { ++$
+ag; }
          elsif (($genome[$i] eq 'g') && ($genome[$i+1] eq 'a')) { ++$
+ga; }
          elsif (($genome[$i] eq 'g') && ($genome[$i+1] eq 'g')) { ++$
+cc; }
          elsif (($genome[$i] eq 'g') && ($genome[$i+1] eq 'c')) { ++$
+gc; }
          elsif (($genome[$i] eq 'g') && ($genome[$i+1] eq 't')) { ++$
+ac; }

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In reply to how can I speed up this perl?? by Anonymous Monk

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