Dear hv,
Sorry for having have to come back to you again. How can I extend your code above, such that it can handle the target which is also ambiguous like this: 
my $source1  = '[TCG]GGGG[AT]'; # ambiguous
my $target1   = 'AGGGG[CT]'; # No of mismatch = 1  only at position 1

[download]
Also the size of source and target will be the same. I tried this: 
sub mismatches {
    my($source, $target) = @_;
    my @sparts = ($source =~ /(\[.*?\]|.)/g);
    my @tparts = ($target =~ /(\[.*?\]|.)/g);
    
    scalar grep $tparts[$_] !~ /^$sparts[$_]/, 0 .. $#sparts;
  }

[download]
But doesn't work. Where did I go wrong?

Regards,
Edward

In reply to Re^2: Mismatch Positions of Ambiguous String by monkfan
in thread Mismatch Positions of Ambiguous String by monkfan

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