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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Quesneville H, Nouaud D, Anxolabéhère D "Detection of new transposable element families in Drosophila melanogaster and Anopheles gambiae genomes." J Mol Evol, 2003 https://doi.org/10.1007/s00239-003-0007-2
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V. Jamilloux, J. Daron, F. Choulet and H. Quesneville "De Novo Annotation of Transposable Elements: Tackling the Fat Genome Issue" Proceedings of the IEEE, vol. 105, no. 3, pp. 474-481, March 2017 https://doi.org/10.1109/JPROC.2016.2590833
Quesneville H, Bergman CM, Andrieu O, Autard D, Nouaud D, Ashburner M, Anxolabehere D "Combined evidence annotation of transposable elements in genome sequences." PLoS Comput Biol, 2005 https://doi.org/10.1371/journal.pcbi.0010022
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Flutre T, Duprat E, Feuillet C, Quesneville H "Considering transposable element diversification in de novo annotation approaches." PLoS One, 2011 https://doi.org/10.1371/journal.pone.0016526
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PMCID: PMC3031573
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