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?