I am just a normal user of the site. I use it rarely as a training of my coding skills, so no offence taken.

Well, if insertion and deletion are also involved in the edit distance, a simple XOR cannot solve the problem. The graph solution to RNAS would be terribly slow (not only in Perl) and one would run out of time (there is a 5 minutes limit). You have to find a way how to solve the problem without going into representing the graphs at all. That was what took me some time, once I knew the algorithm, the implementation was a routine.

It is true that most of the simpler problems can be solved by one-liners in Perl. The site does not care about how you solve the problems: you just download the test data and have 5 minutes to upload the solution. That gives us Perlers an easier start on the ladder.

I agree with you that the jargon used by some bioinformaticians is incomprehensible. I fear the reason sometimes is they do not understand the underlying problems in proper detail, it is just a form of handwaving.

لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ

In reply to Re^5: genetic algorithm for motif finding by choroba
in thread genetic algorithm for motif finding by shakehands

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.