Where to get consensus sequences of human transposable elements
0
2
Entering edit mode
3.6 years ago

I am looking for consensus sequences for human transposable elements (LINE, SINE, SVA, ERV, and more detailed Alu, L1, LTR retrotransposons, etc), and it seems RepBase would be the place to get these. Unfortunately, as they changed to a subscription model, I can't afford to pay 2000 euro for that. Are there other sources that could help me?

database transposons reference • 1.4k views
ADD COMMENT
1
Entering edit mode

Not an answer but a comment: I use this file:

https://github.com/GeneDx/scramble/blob/master/cluster_analysis/resources/MEI_consensus_seqs.fa

There are only 3 of them, however, they cover the most of the "active" human retrotransposons...

ADD REPLY
0
Entering edit mode

Thanks! That's a fairly good start.

ADD REPLY
1
Entering edit mode

Just for someone stumbling upon this thread, I found this embl file which is a start: https://www.dfam.org/releases/Dfam_3.3/families/Dfam_curatedonly.embl.gz

ADD REPLY
0
Entering edit mode

I came here to say dfam. : )

ADD REPLY

Login before adding your answer.

Traffic: 2606 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6