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TE Annotation Collection

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@AndrewChen116 AndrewChen116 released this 08 Jun 06:43
TE_annotation
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This release provides a curated collection of transposable element (TE) annotation files compatible with the PeTEM pipeline, including 18 species across animals, plants, and fungi.

Included species

Kingdom Species File
Animal Homo sapiens human_TE.txt
Animal Mus musculus mouse_TE.txt
Animal Danio rerio zebrafish_TE.txt
Animal Drosophila melanogaster fruit_fly_TE.txt
Plant Arabidopsis thaliana Arabidopsis_TE.txt
Plant Oryza sativa rice_TE.txt
Plant Zea mays maize_TE.txt
Plant Glycine max soybean_TE.txt
Fungi Botrytis cinerea Botrytis_cinerea_TE.txt
Fungi Blumeria graminis Blumeria_graminis_TE.txt
Fungi Colletotrichum higginsianum Colletotrichum_higginsianum_TE.txt
Fungi Leptosphaeria maculans Leptosphaeria_maculans_TE.txt
Fungi Melampsora larici-populina Melampsora_larici-populina_TE.txt
Fungi Magnaporthe oryzae Magnaporthe_oryzae_TE.txt
Fungi Microbotryum violaceum Microbotryum_violaceum_TE.txt
Fungi Puccinia graminis f. sp. tritici Puccinia_graminis_TE.txt
Fungi Sclerotinia sclerotiorum Sclerotinia_sclerotiorum_TE.txt
Fungi Tuber melanosporum Tuber_melanosporum_TE.txt

Download

wget https://github.com/PaoyangLab/PeTEM/releases/download/TE_annotation/TE_files.tar.gz
tar -xzvf TE_files.tar.gz

File format

All files follow the standardized PeTEM TE annotation format:

Column Description
TE_name TE identifier
chromosome Chromosome or scaffold name
start Start coordinate
end End coordinate
score Annotation score
strand Strand information (+, -, or .)
TE_family TE family classification

Example:

AT1TE00010  Chr1  11897  11976  0  +  LTR/Copia
AT1TE00020  Chr1  16883  17009  0  -  RC/Helitron
AT1TE00025  Chr1  17024  18924  0  +  RC/Helitron
AT1TE00030  Chr1  18331  18642  0  -  DNA/HAT

Notes

  • TE annotations were collected from publicly available genome resources and curated into a unified format.
  • The fungal TE annotations are derived from the URGI fungal transposable element database.
  • These files can be used directly as input for the PeTEM pipeline without additional preprocessing.
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