How do I get repeating regions from fasta file or directly from internet
If I go to ncbi site, apply customize view -> Customize -> All features -> Update view and then ctrl + f : Alu.. I can get all alu repeaing regions coordinates from this chromosome.
It looks like:
repeat_region complement(37490..37800)
/note="AluY"
/rpt_family="SINE/Alu"
/rpt_type=DISPERSED
How could I download all this coordinates and names of repeating regions from the internet to .txt file? Or some tool
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alexey.volosnikov •
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http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/simpleRepeat.txt.gz ?
Is there some description for values given, name of repeat (alu, L1 or other name)? And what is it animal for?
Sounds like Repbase is what you need. If you are an academic user you can access it at this link.