<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>

CC BY-SA 4.0
2019-06-06T13:48:11.893Z
2019-06-06T13:48:11.893Z
Devon Ryan
<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>

CC BY-SA 4.0
2019-06-06T02:03:21.207Z
2019-06-06T06:59:11.733Z
2019-06-06T06:59:11.733Z
Jack
<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>

CC BY-SA 4.0
2019-06-08T17:45:52.017Z
2019-06-08T17:45:52.017Z
rroutsong
<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>

CC BY-SA 4.0
2022-05-26T02:24:34.043Z
2022-05-26T02:24:34.043Z
mohan nadiga
<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>

<repeat-elements><repeatmasker><repeat>
Looking for a good tool for repeat masking in long sequences
# 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

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## 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.


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### 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.


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### 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.


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### 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)


---

