Whilst orders of magnitude faster, as posted, your solution is missing some possibilities.

Given the input of:

$seq1 = 'AAAACCCCGGGGTTTT';
$seq2 = 'ACGTACGTACGTACGT';

[download]

It should produce 12 counts:

{  
    A2C => 1,  A2G => 1,  A2T => 1,  C2A => 1,  C2G => 1,  C2T => 1,  
    G2A => 1,  G2C => 1,  G2T => 1,  T2A => 1,  T2C => 1,  T2G => 1,
}

[download]

But only produces the following eight:

A2G=1; G2A=1; C2T=1; T2C=1; A2T=1; A2C=1; G2T=1; G2C=1.

[download]

I'm sure that this is eminently fixable.

With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'
Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.

The start of some sanity?

In reply to Re^2: How can I count the number of substitutions of one letter in a string by another letter in the other string? by BrowserUk
in thread How can I count the number of substitutions of one letter in a string by another letter in the other string? by supriyoch_2008

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