To use a hash as all other monks have suggested surely makes your code much more beautiful and structured.

If I speak strictly to the speed problem, the major issue is that you are repeating the [] operation unneccessarily, when you only need it twice. String operation is very expensive.

You should be able to speed your code up, simply by doing this right before your if-else chain: 

my $a = $genome[$i];
my $b = $genome[$i + 1];

[download]

And in the subsequent code, only use $a and $b, not [] operation any more.

This is a direct answer to your speed issue. Don't get me wrong, you still should use hash as your storage, as it not only makes your code more structured, as a matter fact, but also removes the unnecessary usage of [] operation.

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

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