REPET pipeline is a tool to detect, annotation, and analyze repeats in genomic DNA sequences. The REPET algorithm has two separate pipelines, specifically designed for the analysis of transposable elements (TE). 1. TEdenovo pipeline compares a genome to itself using BLASTER and clusters the results using GROUPER, RECON, and PILER that are clustering tools, specific for interspersed repeated sequences. It builds multiples sequence alignments for each of the clusters and classifies each of them by specific transposable element features to create a non-redundant library of consensus sequences. 2. TEannot pipeline uses BLASTER, RepeatMasker, and CENSOR to annotate the library that TEdenovo created. TEannot pipeline also annotates short, simple repeats (SSRs), using TRF, RepeatMasker, and MREPS.
Sequence composition, complexity and repeats; DNA; Nucleic acid structure analysis
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