Question: Where to download human alpha satellite from centromeric regions
3
gravatar for Biomonika (Noolean)
4.7 years ago by
State College, PA, USA
Biomonika (Noolean)3.1k wrote:

Hello, I am trying to find where to download human alpha satellite sequence. So far I have only been able to find one from 1987 paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC306152/pdf/nar00260-0438.pdf 

I know that Karen H. Miga incorporated her Centromere Reference Models into GRCh38, so downloading her predicted sequences of centromeres would also be helpful - if you can point me where to download those. However, alpha satellite (or multiple since they are variable) would be the best.

ADD COMMENTlink modified 4.7 years ago by jotan1.2k • written 4.7 years ago by Biomonika (Noolean)3.1k
0
gravatar for jotan
4.7 years ago by
jotan1.2k
Australia
jotan1.2k wrote:

Have you tried RepBase?

ADD COMMENTlink modified 7 months ago by RamRS27k • written 4.7 years ago by jotan1.2k

Thanks, I downloaded RepBase20.10.fasta.tar.gz and tried to search for "alpha" and "satellite" with no success.

ADD REPLYlink modified 7 months ago by RamRS27k • written 4.7 years ago by Biomonika (Noolean)3.1k

I'm not sure what that file shows but it looks like a random mix of repeats from different organisms. It could be just an update file without original data.

Try going to http://www.girinst.org/repbase/update/browse.php

Then select "Satellite" under the Repeat Class drop-down menu

Then select "Homo Sapien" under the Taxon drop-down menu.

This will give you an option to browse or download all human satellite and/or primate satellite sequences.

ADD REPLYlink modified 7 months ago by RamRS27k • written 4.7 years ago by jotan1.2k
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