Answers.Body: <p>repeatmasker is meant to annotate/mask a genome given a library of known transposable elements. From the project description, I assume you have not done any sequencing on your own. Then, instead of annotating, I think you should find already computed annotations of TEs.</p>
  <p>The alternative to subscription-based repbase is <a href="https://www.dfam.org/" rel="nofollow noreferrer">dfam</a>. And Just looking at their webpage they seem to have an annotation of all individual TEs in <a href="https://www.dfam.org/releases/Dfam_3.3/annotations/hg38/" rel="nofollow noreferrer">hg38</a>. I bet my shoes there will be plenty of TE annotations in human in genome databases too.</p>
  
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Answers.Text: I'll check it out, thanks. Indeed, for now we have sequencing data, but given our analyses we're willing to use them "as is" as they have also been already aligned. Thanks !
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Answers.Text: Thanks @kamil-s-jaron it was definitely helpful. I managed to intersect with what I wanted. My only issue is that I don't really get which type of TE is it. There's plenty (>500) family names in my subset and it's not spontaneously possible to say that BC200 is a type of alu repeat for instance. As you seem to know a lot about this topic, would you have a recommandation to link my findings to a type of TE? (dfam proposes a classification which could actually be helpful, but I couldn't find a way to call back this information ?) thanks
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Answers.Text: Honestly, I don't know. But it's also a completely new question, would you mind opening a new one? Someone else might be able to help you.
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Answers.Text: Thanks, will do that
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Body: <p>I need to annotate human genome with different types of information, amongst them: transposable elements.
  I read about repeatmasker, but what I understood is that it estimates the probability of a sequence to be a transposon based on the sequence and not based on curated database.
  My university does not have access to RepBase (GIRI). I was hoping finding some possibility with biomart but it seems not possible.</p>
  <p>What would be a way to access curated annotation of all kinds of transposable elements (SINE, Alu seq..) within a given genome/genome coordinates?
  My goal is to estimate the link between some measurements we have made on the genome (binned) ( and Shannon entropy is one of them, and probably the less interesting regarding TE). Eventually, I'd like to be able to estimate that measurement X has a correlation with the number of Alu repeats present in the neighbourhood.</p>
  <p>What would be the best way to achieve this?</p>
  
Tags: <repeat-elements><repeatmasker><transposable-elements>
Title: Annotatation of transposable elements / transposons / SINE sequences in human
ThreadText: # Annotatation of transposable elements / transposons / SINE sequences in human
  
  (Asked by: username_0 on 2021-05-10)
  
  I need to annotate human genome with different types of information, amongst them: transposable elements.
  I read about repeatmasker, but what I understood is that it estimates the probability of a sequence to be a transposon based on the sequence and not based on curated database.
  My university does not have access to RepBase (GIRI). I was hoping finding some possibility with biomart but it seems not possible.
  
  What would be a way to access curated annotation of all kinds of transposable elements (SINE, Alu seq..) within a given genome/genome coordinates?
  My goal is to estimate the link between some measurements we have made on the genome (binned) ( and Shannon entropy is one of them, and probably the less interesting regarding TE). Eventually, I'd like to be able to estimate that measurement X has a correlation with the number of Alu repeats present in the neighbourhood.
  
  What would be the best way to achieve this?
  
  **Tags:** repeat-elements, repeatmasker, transposable-elements
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2021-05-10. Score: 3
  
  repeatmasker is meant to annotate/mask a genome given a library of known transposable elements. From the project description, I assume you have not done any sequencing on your own. Then, instead of annotating, I think you should find already computed annotations of TEs.
  
  The alternative to subscription-based repbase is [dfam](https://www.dfam.org/). And Just looking at their webpage they seem to have an annotation of all individual TEs in [hg38](https://www.dfam.org/releases/Dfam_3.3/annotations/hg38/). I bet my shoes there will be plenty of TE annotations in human in genome databases too.
  
  > **Comments:**
  > **username_0**: I'll check it out, thanks. Indeed, for now we have sequencing data, but given our analyses we're willing to use them "as is" as they have also been already aligned. Thanks !  
  > **username_0**: Thanks @username_1-s-username_1 it was definitely helpful. I managed to intersect with what I wanted. My only issue is that I don't really get which type of TE is it. There's plenty (>500) family names in my subset and it's not spontaneously possible to say that BC200 is a type of alu repeat for instance. As you seem to know a lot about this topic, would you have a recommandation to link my findings to a type of TE? (dfam proposes a classification which could actually be helpful, but I couldn't find a way to call back this information ?) thanks  
  > **username_1**: Honestly, I don't know. But it's also a completely new question, would you mind opening a new one? Someone else might be able to help you.  
  > **username_0**: Thanks, will do that  
  
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