Your suggestion will save some, but just some. You've replaced the fetching of a value from walking 4 pointers to walking 2 pointers. That's a peephole optimization; the big gain is to be made by not comparing so much.

Even if you don't want to use a hash, you can still do: 

if    ($genome [$i] eq 'a') {
    if    ($genome [$i + 1] eq 'a') {$aa ++}
    elsif ($genome [$i + 1] eq 'c') {$ac ++}
    elsif ($genome [$i + 1] eq 'g') {$ag ++}
    elsif ($genome [$i + 1] eq 't') {$at ++}
}
elsif ($genome [$i] eq 'c') {
    if    ($genome [$i + 1] eq 'a') {$ca ++}
    elsif ($genome [$i + 1] eq 'c') {$cc ++}
... etc ...

[download]
which reduces the number of comparisons from max 20 to max 5.

Abigail

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

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