Plant_Annotation_TEs | Plant Genome Annotation - Transposable Elements | Data Labeling library

Plant_Annotation_TEs is a Perl library typically used in Artificial Intelligence, Data Labeling applications. Plant_Annotation_TEs has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

Transposable elements (TEs) are prominent features of a plant genome. During a plant genome annotation project, the TEs must be first identified before the structural gene annotation. After a proper TE annotation, all TE-derived regions in the genome must be masked (preferably soft-masked: repeats in lowercase rather than "N" or "X"). EDTA is one of the most powerful and complete TE annotation pipelines. However, EDTA has low power to annotate SINEs and LINEs. Using structural-based methods, the pipeline described here will create a non-redundant SINEs/LINEs library of your species' genome. These libraries can be further supplied to our modified version EDTA of the pipeline (--sine and --line flags). Moreover, it is known that the EDTA pipeline often generates many false positives TE predictions (mainly represented by TIRs elements).To avoid false positives, we developed an adaptation on the EDTA pipeline that tries to lower the false positive prediction of TIR elements. This adapted EDTA version also annotates non-autonomous LTR elements (e.g., LARD, TRIM, TR-GAG, and BARE-2). It comprehensively annotates SINE, LTR, and TIRs elements at their respective lineages. Furthermore, helitron elements are divided into autonomous (containing HEL domain) and non-autonomous (not containing HEL domain). The input is a fasta file containing the plant genome in chromosome-scale (preferably). The final result will be an augmented TE annotation (containing the outputs commonly generated by the EDTA pipeline), an adequately masked genome for structural gene annotation, and a complete TE report showing TE lineages abundances. Since this pipeline can retrieve complete CRM elements, it is possible to figure out the potential centromeric regions using other approaches with the trf tool. Important Notice 1: This pipeline was tested only on Ubuntu 20.20 and was made for Plant Genomes. Important Notice 2: This pipeline could be better and is under development for improvements.