search

oushujun / EDTA

Extensive de-novo TE Annotator
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
GNU General Public License v3.0
331 stars 72 forks source link

How to identify the structure feature of a TE sequence #486

Open leon945945 opened 1 month ago

leon945945 commented 1 month ago

Hi, I have a TE sequence and I want to know its sequence structure feature, like TIR, EN, ORF1, ORF2, LTR, PBS, PPT, gag, pol or other structures. Can EDTA be used to identify these sequence structure?

oushujun commented 1 month ago

Hello,

You can extract this information through different programs. EDTA provides TIR, LTR, and gag, pol information. For EN, ORF1, ORF2, you may use TEsorter. For PBS, PPT, you can use LTR_digest.

Thanks, Shujun