<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>

CC BY-SA 4.0
2021-05-10T12:29:21.633Z
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 !
Bratten
CC BY-SA 4.0
2021-05-10T20:11:05.133Z
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
Bratten
CC BY-SA 4.0
2021-05-11T00:23:29.550Z
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.
Kamil S Jaron
CC BY-SA 4.0
2021-05-12T09:01:29.753Z
Thanks, will do that
Bratten
CC BY-SA 4.0
2021-05-10T11:13:43.347Z
2021-05-10T11:13:43.347Z
Kamil S Jaron
<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>

<repeat-elements><repeatmasker><transposable-elements>
Annotatation of transposable elements / transposons / SINE sequences in human
# 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 @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  
> **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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