Answers.Body: <p><a href="http://www.repeatmasker.org/RMDownload.html" rel="nofollow noreferrer">RepeatMasker</a> can downloaded an run locally. There's then no size limit, though do note that it's quite slow for mammalian-sized sequences (you'll want to split it into chunks and run in parallel in such cases). For a small 500kb sequence that won't pose an issue.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-06-06T13:48:11.893Z
Answers.LastActivityDate: 2019-06-06T13:48:11.893Z
Answers.UserDisplayName: Devon Ryan
Answers.Body: <p><a href="http://www.cbcb.umd.edu/software/RepeatFinder/" rel="nofollow noreferrer">RepeatFinder</a> may suffice by Volfovsky et al. (2001) and is available for download.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-06-06T02:03:21.207Z
Answers.LastActivityDate: 2019-06-06T06:59:11.733Z
Answers.LastEditDate: 2019-06-06T06:59:11.733Z
Answers.UserDisplayName: Jack
Answers.Body: <p>From: <a href="http://meme-suite.org/doc/glam2_tut.html" rel="nofollow noreferrer">http://meme-suite.org/doc/glam2_tut.html</a>, here's a few tools that do various repeat masking tasks.</p>
  
  <blockquote>
    <p>These tools mask various kinds of repeats: <a href="http://www.repeatmasker.org/" rel="nofollow noreferrer">Repeatmasker</a>, <a href="http://www.girinst.org/censor/" rel="nofollow noreferrer">Censor</a>, <a href="ftp://ftp.ncbi.nih.gov/pub/seg/" rel="nofollow noreferrer">seg/pseg/nseg</a>, <a href="http://meme-suite.org/doc/dust.html" rel="nofollow noreferrer">DUST</a>,
        <a href="http://meme-suite.org/doc/purge.html" rel="nofollow noreferrer">XNU</a>, <a href="https://www.liebertpub.com/doi/abs/10.1089/106652703321825955" rel="nofollow noreferrer">DSR</a>, <a href="https://academic.oup.com/bioinformatics/article/22/24/2980/208627" rel="nofollow noreferrer">GBA</a>.</p>
  </blockquote>
  
  <p>Censor, seg/pseg/nseg, dust, DSR all have locally available applications. DSR, GBA, and CAST are algorithms for repeat masking.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-06-08T17:45:52.017Z
Answers.LastActivityDate: 2019-06-08T17:45:52.017Z
Answers.UserDisplayName: rroutsong
Answers.Body: <p>Please use this python program to mask elements -</p>
  <pre><code>dna = input(&quot;Please enter the DNA sequence or chromosome whose repetitive elements need to be masked:&quot;)
  repele = [&quot;aaaa&quot;, &quot;tttt&quot;, &quot;cccc&quot;, &quot;gggg&quot;]
  counter=0
  str1=str(dna)
  for i in repele:
      str1 = str1.replace(repele[counter], &quot;x&quot;)
      counter=counter+1
  print(str1)
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-05-26T02:24:34.043Z
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Answers.UserDisplayName: mohan nadiga
Body: <p>The <a href="http://www.repeatmasker.org/cgi-bin/WEBRepeatMasker" rel="nofollow noreferrer">repeat masker site</a> has a size limit of 90kb. 
  Where can I mask repeats in a 500kb sequence?</p>
  
  <p>Ideally, I need a thorough repeat masking of known and de-novo found repeats of various complexity. I am working on Windows but can access Unix too.</p>
  
Tags: <repeat-elements><repeatmasker><repeat>
Title: Looking for a good tool for repeat masking in long sequences
ThreadText: # Looking for a good tool for repeat masking in long sequences
  
  (Asked by: username_0 on 2019-06-05)
  
  The [repeat masker site](http://www.repeatmasker.org/cgi-bin/WEBRepeatMasker) has a size limit of 90kb.
  Where can I mask repeats in a 500kb sequence?
  
  Ideally, I need a thorough repeat masking of known and de-novo found repeats of various complexity. I am working on Windows but can access Unix too.
  
  **Tags:** repeat-elements, repeatmasker, repeat
  
  
  ---
  
  ## 4 answers
  
  ### Answer by username_1 on 2019-06-06. Score: 4
  
  [RepeatMasker](http://www.repeatmasker.org/RMDownload.html) can downloaded an run locally. There's then no size limit, though do note that it's quite slow for mammalian-sized sequences (you'll want to split it into chunks and run in parallel in such cases). For a small 500kb sequence that won't pose an issue.
  
  
  ---
  
  ### Answer by username_2 on 2019-06-06. Score: 3
  
  [RepeatFinder](http://www.cbcb.umd.edu/software/RepeatFinder/) may suffice by Volfovsky et al. (2001) and is available for download.
  
  
  ---
  
  ### Answer by username_3 on 2019-06-08. Score: 2
  
  From: <http://meme-suite.org/doc/glam2_tut.html>, here's a few tools that do various repeat masking tasks.
  
  > These tools mask various kinds of repeats: [Repeatmasker](http://www.repeatmasker.org/), [Censor](http://www.girinst.org/censor/), [seg/pseg/nseg](ftp://ftp.ncbi.nih.gov/pub/seg/), [DUST](http://meme-suite.org/doc/dust.html),
  > [XNU](http://meme-suite.org/doc/purge.html), [DSR](https://www.liebertpub.com/doi/abs/10.1089/106652703321825955), [GBA](https://academic.oup.com/bioinformatics/article/22/24/2980/208627).
  
  Censor, seg/pseg/nseg, dust, DSR all have locally available applications. DSR, GBA, and CAST are algorithms for repeat masking.
  
  
  ---
  
  ### Answer by username_4 on 2022-05-26. Score: 0
  
  Please use this python program to mask elements -
  
  ```
  dna = input("Please enter the DNA sequence or chromosome whose repetitive elements need to be masked:")
  repele = ["aaaa", "tttt", "cccc", "gggg"]
  counter=0
  str1=str(dna)
  for i in repele:
      str1 = str1.replace(repele[counter], "x")
      counter=counter+1
  print(str1)
  
  ```
  
  
  ---
  
  