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For example, TEs make up nearly half of the human ( Homo sapiens) genome and approximately 85% of the genomes of wheat ( Triticum aestivum) and maize. Originally discovered by Barbara McClintock in maize ( Zea mays), TEs are now known to comprise the majority of genetic material in many eukaryotic genomes. Transposable elements (TEs) are repetitive, mobile sequences found in most eukaryotic genomes analyzed to date. EDTA is open-source and freely available. These annotations will promote a much more in-depth understanding of the diversity and evolution of TEs at both intra- and inter-species levels. The benchmarking results and pipeline developed here will greatly facilitate TE annotation in eukaryotic genomes. Using other model species with curated TE libraries (maize and Drosophila), EDTA is shown to be robust across both plant and animal species. EDTA also deconvolutes nested TE insertions frequently found in highly repetitive genomic regions. Using the most robust programs, we create a comprehensive pipeline called Extensive de-novo TE Annotator (EDTA) that produces a filtered non-redundant TE library for annotation of structurally intact and fragmented elements.
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Performance metrics include sensitivity, specificity, accuracy, precision, FDR, and F 1. We evaluate the performance of methods annotating long terminal repeat (LTR) retrotransposons, terminal inverted repeat (TIR) transposons, short TIR transposons known as miniature inverted transposable elements (MITEs), and Helitrons. We benchmark existing programs based on a carefully curated library of rice TEs. Moreover, a comprehensive pipeline is needed to produce a non-redundant library of TEs for species lacking this resource to generate whole-genome TE annotations. Numerous methods exist for annotation of each class of TEs, but their relative performances have not been systematically compared. Current assemblies traverse transposable elements (TEs) and provide an opportunity for comprehensive annotation of TEs. Sequencing technology and assembly algorithms have matured to the point that high-quality de novo assembly is possible for large, repetitive genomes.