<p>I need to do permutation to 10,000 DNA sequences, the length of which are between 200bp~1000bp. In fact, for each sequence, I only need 5,000 permutations to do Monte-Carlo simulation. However, when perl modules List::Permutor or Algorithm::Permute was applied, I found 5,000 permutations of one sequence were quite similar, which went against my intention of random sampling. And to generate a universal set of permutation then randomly sampling is too time consuming. So my question is: is there a way to do a random permutation?</p>

<p>In fact, all I need to do is to search the enriched motif (5mer-10mer) on the sequence sets. So if there is any program for this, plz tell me :)</p>

<p>Thank you!</p>

How about the <a href="http://emboss.sourceforge.net">EMBOSS</a> program, <a href="http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/shuffleseq.html">shuffleseq</a>?

Description: This takes a sequence as input and outputs one or more sequences whose order has been randomly shuffled. No bases or residues are changed, only their order.

You can run it something like:

    shuffleseq -sequence myseqs.fa -outseq myshuffledseqs.fa -shuffle 5000