Thanks for your response. I don't think the bioinformatics tool HMMER3 (making and using HMMs) can generate a whole shuffled genome sequence based on reading in its intact version.

But if you know of any software package that can do this, that would be good to know

About frequencies of 1 letters, 2 letters etc., REALLY good question - but I think I am happy with simple shuffling, without consideration for frequencies of 2 letters or higher order, because there is no theoretical or empirical indication that it would make a difference while assessing background signal from these shuffled sequences. But I might run that experiment in the future, for curiosity sake :)

In reply to Re^2: Reduce RAM required by onlyIDleft
in thread Reduce RAM required by onlyIDleft

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.