Thanks everyone for chiming in. Many of you were concerned with the number of arrays I was trying to compare, so I am trying an altogether different approach.(sorry if this seems like a somewhat different problem, but it is an all-together different approach to the above mentioned-issue). Another way to deal with my problem is as follows.
I need to evaluate if a pair of strings of the same length are identical after excluding all positions that have an 'N' in one or both strings. Both strings will always consist of the character set /ATGCN
For example, the comparison of $a and $b would meet my criterion:
$a = 'ATGNCNC';
$b = 'ATGACNN';
But $c and $d would not:
$c = 'ATGNCNC';
$d = 'TTGNNNC';
(because the first character differs at a position that does not contain an 'N' in either string)
Again, there is an extreme premium on efficiency here. Any thoughts?