$permutations_total++ while $string =~ $promoters_regex[$j];

[download]

I guess you want: 

$permutations_total++ while $string =~ /$promoters_regex[$j]/g;

[download]

here, otherwise you'll never terminate once there's a match. But now, qr will actually be slower, because you're are interpolating the compiled regex, and recompiling it. And if there are many matches, some gain could be made by writing it as: 

{  no warnings 'numeric';
   $permutations_total += $string =~ /$promoters_regex[$j]/g;
}

[download]

Abigail

In reply to Re: Performance Tuning: Searching Long-Sequence Permutations by Abigail-II
in thread Performance Tuning: Searching Long-Sequence Permutations by Itatsumaki

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