Where to get consensus sequences of human transposable elements
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8 days 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 • 165 views
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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...

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Thanks! That's a fairly good start.

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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

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I came here to say dfam. : )

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