In case performance matters and your sequences are longer, you could also use XOR bit logic in combination with tr///: 

#!/usr/bin/perl -w
use strict;

my @cnt = qw(A2G G2A C2T T2C A2T A2C G2T G2C);
my %cnt;

for my $change (@cnt) {
    my ($c1, $c2) = split /2/, $change;
    $c2 =~ tr/ATCG/HRDZ/;
    my $x = $c1 ^ $c2;
    $cnt{$change} = eval "sub { \$_[0] =~ tr/$x/$x/ }";
}

my $seq1 = "AAAGATCGTG";
my $seq2 = "AGTACTTTCC";

(my $tmp = $seq2) =~ tr/ATCG/HRDZ/;
my $diff = $seq1 ^ $tmp;
    
print join("; ", map { $_."=".$cnt{$_}->($diff) } @cnt ), ".";

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

[download]

The idea here is that XORing two strings produces a different value X for each combination of characters, which you can then count with a simple tr/X/X/.  The additional prior transformation tr/ATCG/HRDZ/ on one of the strings is required because the XOR operation would otherwise produce symmetric/undirected results, i.e. A2G would be indistinguishable from G2A, etc.

(Just in case it isn't clear:  the %cnt hash doesn't hold the count results, but rather the subs doing the respective tr/X/X/ counting.)

In reply to Re: How can I count the number of substitutions of one letter in a string by another letter in the other string? by Eliya
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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