Here is an easy one for all of you gurus. There is a premium on efficiency as I need to conduct the following operation on approximately 1 X 10^8 comparisons. 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?

In reply to simple string comparison for efficiency by CaptainF

Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post; it's "PerlMonks-approved HTML":

  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.