If your two sequences are always the exact same length and you simply want to compare equivalent positions (I think I'm understanding that correctly), you may want to simply store each sequence each as their own simple scalar string and make use of the substr function for comparison of positions. That way you could query the position alone and have it return which protein is in that position in both strings.

Admittedly, I could be oversimplifying the problem if I've misunderstood.

I love it when things get difficult; after all, difficult pays the mortgage. - Dr. Keith Whites
I hate it when things get difficult, so I'll just sell my house and rent cheap instead. - perldigious

In reply to Re: Per residue sequence alignment - per character string comparison? by perldigious
in thread Per residue sequence alignment - per character string comparison? by proteins

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.