Fig. 4: Identification of TEs with fine-grained TE boundaries based on O. sativa. | Nature Communications

Fig. 4: Identification of TEs with fine-grained TE boundaries based on O. sativa.

From: HiTE: a fast and accurate dynamic boundary adjustment approach for full-length transposable element detection and annotation

Fig. 4

a Pipeline of HiTE for identifying TIR and Helitron elements. Searching for confident structures reveals the true ends of TIR and Helitron elements. The robust evidence of real TEs is checked by non-homology flanking regions of multiple sequence alignment. b, c Evaluation of HiTE against HiTE-FMEA using BM_HiTE and BM_RM2 under rough and precise perfect definitions, respectively. d Evaluation of HiTE-TIR against HiTE-TIR-NoFiltering, EDTA-TIR, EDTA-TIR-NoFiltering, and RepeatModeler2 using BM_HiTE. e Evaluation of HiTE-Helitron against HiTE-Helitron-NoFiltering, EDTA-Helitron, EDTA-Helitron-NoFiltering, RepeatModeler2, and EAHelitron using BM_HiTE. TIR: terminal inverted repeat; TSDs: target site duplications; Pe: Perfect; Go: Good; Pr: Present; NF: Not_found. Sen: Sensitivity; Pre: Precision; FDR: False discovery rate; F1: F1-score.

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