UPDATE: I tried InjunJoel's approach, and it blazed through all 6.5 million bases very quickly. I now see that using regexps for this type of problem is not the way to go... could someone perhaps explain to me precisely why the regexp approach that I initially tried brought my machine to a screeching halt? I presume it is has something to do with the way it stores the string in memory while traversing it with the regexp....

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Hello,

I have a massive DNA sequence ( a string of ~600,000 (CORRECTION: 6.5million) "A"s "G"s "C"s and "T"s ) and I need to count the number of occurences of every possible 1, 2, and 3 letter combination in this sequence. I'm trying to use the following approach:

while ( $seq =~ /$term/g ) { $count++; }

Unfortunately, this is proving prohibitively slow. I would greatly appreciate any advice on how to speed this up (I tried adding /o, but it made little to no difference).

Also, while I have your ear, I was wondering if anyone could tell me how I can use a variable in a tr// regexp?

Thanks!

In reply to Question about speeding a regexp count by Commander Salamander

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