One immediate saving that leaps out at me is that you can replace this 

while ($sub =~ /([GCATN])/g) {
   if ($1 eq 'G') { $bases{g}++; }
   if ($1 eq 'C') { $bases{c}++; }
   if ($1 eq 'A') { $bases{a}++; }
   if ($1 eq 'T') { $bases{t}++; }
   if ($1 eq 'N') { $bases{n}++; }
}

[download]

with 

$bases{ lc($1) }++ while $sub =~ /[GCATN])/g;

[download]

Which should speed that bit up. If you can live with your keys being uppercase rather than lower, omit the call to lc. I realise that isn't the major part of time though.

When you dealing with such long strings and especially if you are matching against them multiple times, then studying the string can make a remarkable difference. I'm not sure if this is true where the string contains so few unique characters, but it would be worth testing.

Examine what is said, not who speaks.
"Efficiency is intelligent laziness." -David Dunham
"When I'm working on a problem, I never think about beauty. I think only how to solve the problem. But when I have finished, if the solution is not beautiful, I know it is wrong." -Richard Buckminster Fuller


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

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