text: user522: I'm looking for a way to identify low complexity regions and other repeats in the genome of Escherichia coli. I found that RepeatMasker may be used for example when drafting genomes of prokaryotes (E. coli example). But RepeatMasker works on a limited dataset of species, neither of them being prokaryotes. By default, when running RepeatMasker, if no species is specified, it will compare with homo sapiens data. 
  This seems rather inadequate, but the most relevent alternative, PRAP, requires a "dead" tool (VisCoSe, by Michael Spitzer).
  
  Is it still wise to to use RepeatMasker on Escherichia coli?
  If yes, which settings would maximise relevance ?
  
  
  user294: From your comment, it seems that masking regions are not your priority, but you would rather find them (correct me if I am wrong):
  
  not interested in masking, but really finding any type of repeats, from low complexity regions to small repeats
  
  To find these regions, you can try RepeatFinder. From their paper, it seems that is suitable for bacterial genomes too. It also seems to be faster because based on suffix tree data structure instead of working with string-matching algorithm (as in RepeatMasker).  
  
  user123: If I understood correctly your question, you want to mask those regions in a (FASTA?) genome. I think you could identify those regions using mummer and mask them using bedtools.
  # align genome against itself
  nucmer --maxmatch --nosimplify genome.fasta genome.fasta
  
  # select repeats and convert the corrdinates to bed format
  show-coords -r -T -H out.delta | awk '{if ($1 != $3 && $2 != $4) print $0}' | awk '{print $8"\t"$1"\t"$2}' > repeats.bed
  
  # mask those bases with bedtools
  bedtools maskfasta -fi genome.fasta -bed repeats.bed -fo masked.fasta
  
  Have a look at nucmer and bedtools maskfasta options to fine-tune your analysis.
  
original_text: 522: <p>I'm looking for a way to identify low complexity regions and other repeats in the genome of <em>Escherichia coli</em>. I found that RepeatMasker may be used for example when drafting genomes of prokaryotes (<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587949/" rel="nofollow noreferrer"><em>E. coli</em> example</a>). But RepeatMasker works on a limited dataset of species, neither of them being prokaryotes. By default, when running RepeatMasker, if no species is specified, it will compare with homo sapiens data. </p>
  
  <p>This seems rather inadequate, but the most relevent alternative, <a href="https://sites.google.com/site/prapsoftware/" rel="nofollow noreferrer">PRAP</a>, requires a "dead" tool (VisCoSe, by Michael Spitzer).</p>
  
  <ol>
  <li>Is it still wise to to use RepeatMasker on <em>Escherichia coli</em>?</li>
  <li>If yes, which settings would maximise relevance ?</li>
  </ol>
   294: <p>From your comment, it seems that masking regions are not your priority, but you would rather find them (correct me if I am wrong):</p>
  
  <blockquote>
    <p>not interested in masking, but really finding any type of repeats, from low complexity regions to small repeats</p>
  </blockquote>
  
  <p>To find these regions, you can try <a href="http://www.cbcb.umd.edu/software/RepeatFinder/" rel="nofollow noreferrer">RepeatFinder</a>. From their <a href="http://www.cbcb.umd.edu/software/RepeatFinder/RepeatFinderReprint.pdf" rel="nofollow noreferrer">paper</a>, it seems that is suitable for bacterial genomes too. It also seems to be faster because based on suffix tree data structure instead of working with string-matching algorithm (as in RepeatMasker).  </p>
   123: <p>If I understood correctly your question, you want to mask those regions in a (FASTA?) genome. I think you could identify those regions using <a href="http://mummer.sourceforge.net/" rel="nofollow noreferrer">mummer</a> and mask them using <a href="http://bedtools.readthedocs.io/en/latest/" rel="nofollow noreferrer">bedtools</a>.</p>
  <pre><code># align genome against itself
  nucmer --maxmatch --nosimplify genome.fasta genome.fasta
  
  # select repeats and convert the corrdinates to bed format
  show-coords -r -T -H out.delta | awk '{if (<span class="math-container">$1 != $</span>3 &amp;&amp; <span class="math-container">$2 != $</span>4) print <span class="math-container">$0}' | awk '{print $8"\t"$1"\t"$</span>2}' &gt; repeats.bed
  
  # mask those bases with bedtools
  bedtools maskfasta -fi genome.fasta -bed repeats.bed -fo masked.fasta
  </code></pre>
  <p>Have a look at <a href="http://mummer.sourceforge.net/manual/#identifyingrepeats" rel="nofollow noreferrer">nucmer</a> and <a href="http://bedtools.readthedocs.io/en/latest/content/tools/maskfasta.html" rel="nofollow noreferrer">bedtools maskfasta</a> options to fine-tune your analysis.</p>
  