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zhangrengang / TEsorter

TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes
https://doi.org/10.1093/hr/uhac017
GNU General Public License v3.0
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Can TEsorter classify Class II elements(DNA transposons) into clade-level? #47

Open 2eYu opened 1 year ago

2eYu commented 1 year ago

Hi @zhangrengang As the title, my TEsorter version is 1.4.6, I use TEsorter to classify my EDTA's outcome(my interested species is an apple species). my code: TEsorter Gala_genome.fa.mod.EDTA.intact.fa -db rexdb-plant -p 5 and I got this file, Gala_genome.fa.mod.EDTA.intact.fa.rexdb-plant.cls.tsv, I saw Copia and other superfamily-level LTR TEs divided into so many clades, such as Ogre, Ale, etc.. But, none superfamily in TIR Oder could be classified into clade level. If I want to obtain Class II elements in clade-level, could you please give me some advice to achieve it?

Best wishes~

zhangrengang commented 1 year ago

Hi @2eYu No, TEsorter cannot classify TIR into clade-level. It is because there are no curated clade-level classifications for TIR and all other non-LTR elements, to my knowledge. If you are interested in it, you may build a clade-level classification for TIR, and I will be happy to add the database to TEsorter.

acontrerasg commented 8 months ago

Hello, I just want to bring to your attention @zhangrengang this preprint that creates a clade level classificaiton of DNA transposons DDE transposases : preprint_link In case you woudl like to take a look.