Clever mapping of the characters in one of the strings could work around the problems with the XOR approach.  For example, using tr/ATCG/HRDZ/: 

my %change;  # reverse lookup table
my @t = qw(A T C G);
for my $t1 (@t) {
    for my $t2 (@t) {
        my $t = $t2;
        $t =~ tr/ATCG/HRDZ/;
        $change{ $t1 ^ $t } = "$t1->$t2";
    }
}

sub diff {
    my ($target, $str) = @_;
    $str =~ tr/ATCG/HRDZ/;
    my $diff = $target ^ $str;
    while ($diff =~ /([^\x09\x06\x07\x1d])/g) {
        printf "  %d: %s\n", pos($diff), $change{$1};
    }
}

my $target = "ATTCCGGG";

for (qw(ATTGCGGG ATACCGGC)) {
    print "\n$target\n$_\n";
    diff($target, $_);
}

__END__

ATTCCGGG
ATTGCGGG
  4: C->G

ATTCCGGG
ATACCGGC
  3: T->A
  8: G->C

[download]

The reverse lookup table just needs to be set up once, and the remaining operations (string bit operation, tr///, m//g) should all be pretty fast.

(As the keys in the lookup table are integers < 256, you could in theory also set up an array, and use the xor value as the index.)

In reply to Re: mismatching characters in dna sequence by Eliya
in thread mismatching characters in dna sequence by prbndr

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