Annotatation of transposable elements / transposons / SINE sequences in human 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?
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.