Beefy Boxes and Bandwidth Generously Provided by pair Networks
No such thing as a small change

Comment on

( #3333=superdoc: print w/replies, xml ) Need Help??
Since you appear to have nucleic acid strings, perhaps you could leverage the minimal alphabet used to pre-compute differences. Assuming each position can only be represented by 5 characters (A, C, T, G and -) then taking 4 characters at a time, there can only be 625 possible strings. Comparing two such sub strings means there are only 390,625 possible pairs - surely small enough to fit into memory.

I do realize that you have to keep track of which "quad" you are comparing so that your position comes out right but this is hardly significant. Even comparing 5 characters at a time is less than 10 million parings so depending on your memory constraints you may not be limited to quads. Of course, if your strings can have more than 5 characters at each position you will have to do fewer at a time.

If you need an implementation of this, let me know but I think it should be fairly obvious.

Cheers - L~R

In reply to Re: Fast Identification Of String Difference by Limbic~Region
in thread Fast Identification Of String Difference by neversaint

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.
  • Log In?

    What's my password?
    Create A New User
    and all is quiet...

    How do I use this? | Other CB clients
    Other Users?
    Others imbibing at the Monastery: (8)
    As of 2017-12-15 09:38 GMT
    Find Nodes?
      Voting Booth?
      What programming language do you hate the most?

      Results (425 votes). Check out past polls.