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REPET

REPET

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.

Topic

Sequence composition, complexity and repeats; DNA; Nucleic acid structure analysis

Details

  • Operation: Repeat sequence detection; Repeat sequence analysis
  • Software interface: Command-line user interface
  • Language: Python
  • Operating system: Linux
  • License: CeCILL license
  • Cost: Free
  • Version name: 3.0
  • Maturity: Mature
  • Credit: Institut national de la recherche agronomique, the TransPLANT FP7
  • Contact: urgi-repet _at_ versailles.inra.fr
  • Collection: -

Publications

Hoede C, Arnoux S, Moisset M, Chaumier T, Inizan O, Jamilloux V, Quesneville H "PASTEC: an automatic transposable element classification tool." PLoS ONE 2014; 9(5):e91929 https://doi.org/10.1371/journal.pone.0091929
PMID: 24786468
PMCID: PMC4008368


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
PMID: 15008403
PMCID: None


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
PMID: 16110336
PMCID: PMC1185648


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
PMID: 21304975
PMCID: PMC3031573


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