This is the same as what you're doing, but using s/// to walk the template.

my $a = "ABABA";
my $b = "BB--B-BB";
my $new = $b;
my $a_pos = 0;
$new =~ s:[^-]:substr($a, $a_pos++, 1):ge;
print "New is $new\n";
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Update: I like this better. Inserting hyphens at corresponding points:

my $a = "ABABA";
my $b = "BB--B-BB";
substr($a, pos($b)-1, 0, '-') while ($b =~ /-/g);

print "A is now $a\n";
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