You're recompiling those regexes every time through the loop, which is fairly expensive. Use the "qr" syntax to create compiled regexes in the @promoters_regex array, thusly: 

$promoters_regex[0] = qr/[NT][GCATN][NG][NC][NG][NT][NG]/;
$promoters_regex[1] = qr/[NG][NT][NG][NC][NG][GCATN][NT]/;
$promoters_regex[2] = qr/[NA][GCATN][NC][NG][NC][NA][NC]/;
$promoters_regex[3] = qr/[NC][NA][NC][NG][NC][GCATN][NA]/;
...
$permutations_total++ while $string =~ $promoters_regex[$j];

[download]

You would also find it a bit faster if you could combine all the regexes into a big alternative regex, but then you couldn't match multiple promoters that overlap each other so that's probably gonna require lookaheads of some kind. Hm....

PS: Most of the time when you write a for loop with an index iterating through the elements of an array, you'd be better off with a foreach loop. This is one of those cases: 

    for (@promoters_regex) {
        $total++ while $string =~ $_;
    }

[download]

    -- Chip Salzenberg, Free-Floating Agent of Chaos

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

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