Body: <p>I have a hundred insect genomes and I'm looking for <code>repeated regions</code> along these <code>assemblies</code>.</p>
  <p>First of all, I thought of using <code>RepeatModeler</code>, only the most familiar among you know that it is not at all optimized software that requires a lot of resources and calculation time, which is therefore not feasible in my case.</p>
  <p>One possible solution <code>Repbase</code> is not free.</p>
  <p>I thought for example to use a <code>blastn</code> approach by using in query the assemblages and in database of nucleotide databases containing <strong>ETs</strong>, which would be an approach maybe less sensitive but much faster! Only I can't find a database in ET representative of <code>eukaryotes</code></p>
  <p>I have two questions:</p>
  <ul>
  <li>Is there an alternative algorithm that is fast enough to process a large number of insect genomes?</li>
  <li>Is there a database of representative ETs to enable a <code>blastn</code> style solution?</li>
  </ul>
  <p>Thanks a lot.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-15T18:06:43.030Z
Comments.Text: when you say "ET" do you mean "TE" ("transposable element")? If not, what does that abbreviation stand for?
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-12-16T08:34:26.093Z
Comments.Text: Yes Transposable element sorry
Comments.UserDisplayName: Grendel
Tags: <assembly><repeat-elements><repeat>
Title: Repeat analysis on eukaryotic assemblies
ThreadText: # Repeat analysis on eukaryotic assemblies
  
  (Asked by: username_0 on 2020-12-15)
  
  I have a hundred insect genomes and I'm looking for `repeated regions` along these `assemblies`.
  
  First of all, I thought of using `RepeatModeler`, only the most familiar among you know that it is not at all optimized software that requires a lot of resources and calculation time, which is therefore not feasible in my case.
  
  One possible solution `Repbase` is not free.
  
  I thought for example to use a `blastn` approach by using in query the assemblages and in database of nucleotide databases containing **ETs**, which would be an approach maybe less sensitive but much faster! Only I can't find a database in ET representative of `eukaryotes`
  
  I have two questions:
  
  * Is there an alternative algorithm that is fast enough to process a large number of insect genomes?
  * Is there a database of representative ETs to enable a `blastn` style solution?
  
  Thanks a lot.
  
  **Tags:** assembly, repeat-elements, repeat
  
  > **Comments:**
  > **username_1**: when you say "ET" do you mean "TE" ("transposable element")? If not, what does that abbreviation stand for?  
  > **username_0**: Yes Transposable element sorry  
  
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  ## 0 answers
  
  