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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?

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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. And Just looking at their webpage they seem to have an annotation of all individual TEs in hg38. I bet my shoes there will be plenty of TE annotations in human in genome databases too.

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  • $\begingroup$ 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 ! $\endgroup$
    – Bratten
    May 10, 2021 at 12:29
  • $\begingroup$ 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 $\endgroup$
    – Bratten
    May 10, 2021 at 20:11
  • $\begingroup$ 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. $\endgroup$
    – Kamil S Jaron
    May 11, 2021 at 0:23
  • $\begingroup$ Thanks, will do that $\endgroup$
    – Bratten
    May 12, 2021 at 9:01

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