Answers.Body: <p>Would advise doing Denovo identification method structure-based. Then use these public databases (  RepBase, Dfam ) to look for high similarity or homology exploration, this possibility if your species, the repeats not yet discovered, or deposited in the databases.</p>
  
  <p>If the species well-investigated earlier and the mobile element recognised, I assume it will be a straightforward task using species-specific search via Repeatmasker tool with the -species flag to obtain the MobileElement annotation in the genome.</p>
  
  <p>Let me know if you need any data from Repbase related to your species, i have an entree. </p>
  
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Answers.Text: Thanks! This is a great answer. For how long has RepBase been subscriber-only?
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Answers.Text: I think the middle of last year
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Answers.Body: <p>Back in the Day™ <a href="http://www.repeatmasker.org/" rel="nofollow noreferrer">RepeatMasker</a><sup>[1]</sup> was the go-to tool everyone used for TE annotation in eukaryotes. At the time, the <a href="https://www.girinst.org/repbase/" rel="nofollow noreferrer">RepBase database from GIRI</a><sup>[2]</sup> (license required) was the <em>de facto</em> database recommended for RepeatMasker users. I know <em>de facto</em> isn't necessarily <em>definitive</em>, but it may have been the only public database supported for some time.</p>
  
  <p>It looks like <a href="https://github.com/rmhubley/RepeatMasker#libraries-overview" rel="nofollow noreferrer">more recent efforts</a> have focused on developing the <a href="https://dfam.org/home" rel="nofollow noreferrer">Dfam database</a>, mirrored after the design of databases like Pfam and Rfam.</p>
  
  <hr>
  
  <p><sup>[1]</sup>Smit AFA, Hubley R, Green P (2013-2015) RepeatMasker Open-4.0, <a href="http://www.repeatmasker.org" rel="nofollow noreferrer">http://www.repeatmasker.org</a>. </p>
  
  <p><sup>[2]</sup>Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J (2005) Repbase Update, a database of eukaryotic repetitive elements. <em>Cytogentic and Genome Research</em> 110:462-467, <a href="https://doi.org/10.1159/000084979" rel="nofollow noreferrer">doi:10.1159/000084979</a>.</p>
  
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Answers.Text: Thanks for the answer. So, if I understand correctly, the strengths of the Dfam database over RepeatMasker is that it's more extensive?
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Body: <p>This isn't quite my speciality, but I've been tasked with finding any evidence of Mobile Genetic Elements (like transposable elements, retrotransposons, bacteriophages, etc.) within some WGS samples. </p>
  
  <p>Is there a "definitive" database used with sequences? How "species-specific" would this be?</p>
  
  <p>Furthermore, are there standard algorithms used to find these MGEs? I suspect we don't have a comprehensive database of all possible MGEs, but it may be possible to query against the sequences we do indeed have (or detect any repetitive elements within the genome). </p>
  
Tags: <blast><repeat-elements><transposable-elements><bacteria>
Title: Is there a "definitive" database for Mobile Genetic Elements?
ThreadText: # Is there a "definitive" database for Mobile Genetic Elements?
  
  (Asked by: username_0 on 2020-02-19)
  
  This isn't quite my speciality, but I've been tasked with finding any evidence of Mobile Genetic Elements (like transposable elements, retrotransposons, bacteriophages, etc.) within some WGS samples.
  
  Is there a "definitive" database used with sequences? How "species-specific" would this be?
  
  Furthermore, are there standard algorithms used to find these MGEs? I suspect we don't have a comprehensive database of all possible MGEs, but it may be possible to query against the sequences we do indeed have (or detect any repetitive elements within the genome).
  
  **Tags:** blast, repeat-elements, transposable-elements, bacteria
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2020-02-20. Score: 2
  
  Would advise doing Denovo identification method structure-based. Then use these public databases ( RepBase, Dfam ) to look for high similarity or homology exploration, this possibility if your species, the repeats not yet discovered, or deposited in the databases.
  
  If the species well-investigated earlier and the mobile element recognised, I assume it will be a straightforward task using species-specific search via Repeatmasker tool with the -species flag to obtain the MobileElement annotation in the genome.
  
  Let me know if you need any data from Repbase related to your species, i have an entree.
  
  > **Comments:**
  > **username_0**: Thanks! This is a great answer. For how long has RepBase been subscriber-only?  
  > **username_1**: I think the middle of last year  
  
  ---
  
  ### Answer by username_2 on 2020-02-20. Score: 1
  
  Back in the Day™ [RepeatMasker](http://www.repeatmasker.org/)[1] was the go-to tool everyone used for TE annotation in eukaryotes. At the time, the [RepBase database from GIRI](https://www.girinst.org/repbase/)[2] (license required) was the *de facto* database recommended for RepeatMasker users. I know *de facto* isn't necessarily *definitive*, but it may have been the only public database supported for some time.
  
  It looks like [more recent efforts](https://github.com/rmhubley/RepeatMasker#libraries-overview) have focused on developing the [Dfam database](https://dfam.org/home), mirrored after the design of databases like Pfam and Rfam.
  
  ---
  
  [1]Smit AFA, Hubley R, Green P (2013-2015) RepeatMasker Open-4.0, <http://www.repeatmasker.org>.
  
  [2]Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J (2005) Repbase Update, a database of eukaryotic repetitive elements. *Cytogentic and Genome Research* 110:462-467, [doi:10.1159/000084979](https://doi.org/10.1159/000084979).
  
  > **Comments:**
  > **username_0**: Thanks for the answer. So, if I understand correctly, the strengths of the Dfam database over RepeatMasker is that it's more extensive?  
  
  ---
  
  