Depending on the length and number of your nucleic acids, and the number of comparisons you are making it might be better to store and compare bit strings generated with the vec command rather than character strings. You could convert each character in the original string with a for loop and a hash table ie something like 
my $char_string = "AAATAT";
my $bit_string = "";
my %lookup_table  = ("A" => "00", "T" => "01", "C" => "10", "G" => "11
+");

my @char_array=(split //, $char_string);
for (my $i=0; $i <= $#char_array ; $i++) {
   vec($bit_string,$i,2) = $lookup_table{$char_array[$i]};
   }

[download]

In reply to Re^2: Hamming Distance Between 2 Strings - Fast(est) Way? by b_hall
in thread Hamming Distance Between 2 Strings - Fast(est) Way? by monkfan

Title:
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, details, 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, summary, 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.