Question: Where to download human alpha satellite from centromeric regions
3
gravatar for Biomonika (Noolean)
4.0 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 4.0 years ago by jotan1.2k • written 4.0 years ago by Biomonika (Noolean)3.1k
0
gravatar for jotan
4.0 years ago by
jotan1.2k
Australia
jotan1.2k wrote:

Have you tried RepBase?

http://www.girinst.org/server/RepBase/index.php

 

ADD COMMENTlink written 4.0 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 written 4.0 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.

http://imgur.com/qM0sgSD

 

 

 

 

 

 

ADD REPLYlink written 4.0 years ago by jotan1.2k
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