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REPET

Repet illustration

REPET


 

The REPET package ( Flutre et al, 2011 ) integrates bioinformatics programs in order to tackle biological issues at the genomic scale. It is distributed under the CeCILL license and deposited to the Agence de Protection des Programmes ( APP ) under the Inter Deposit Digital Number FR 001 480007 000 R P 2008 000 31 235. It is also registered here on the Plume web site.

To download the last  REPET package v2.2


Its two main pipelines are dedicated to detecte, annotate and analyse repeats in genomic sequences, specifically designed for transposable elements (TEs).

  •  TEdenovo: this pipeline starts by comparing the genome with itself using BLASTER. Then it clusters matches with GROUPER, RECON and PILER, clustering programs specific for interspersed repeats. For each cluster, it builds a multiple alignment from which a consensus sequence is derived. Finally these consensus are classified according to TE features and redundancy is removed. At the end we obtain a library of classified, non-redundant consensus sequences.
TE de novo pipeline
  • TEannot: this pipeline mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, using BLASTER, RepeatMasker and CENSOR. An empirical statistical filter is applied to discard false-positive matches. Short simple repeats (SSRs) are annotated along the way with TRF, RepeatMasker and MREPS. Then the pipeline chains, with MATCHER via dynamic programming, TE fragments belonging to the same, disrupted copy. A "long join" procedure is subsequently applied to connect distant fragments. Finally annotations are exported into GFF3 and gameXML files.
TE_Annot illustration

 

Repet v2.2 package also contains:

  • SegDup pipeline to detect segmental duplications in genomic sequences ( Fiston-Lavier et al. 2007 )
  • TallymerPipe pre-processing tool for a fast detection of repeated regions
  • SATannot pipeline to detect tadem repeats
  • PASTEClassifier classifies TEs based on Wicker et al classification

All tool cards are ongoing.

Prerequisites and installation notes are described in README  

Optional but much advised, you will need Repbase, the well-known library of repeats. To obtain it, go to http://www.girinst.org/server/RepBase/index.php ; you will find there a file specially formatted for REPET ("REPET edition"). Today the last version is RepBase 17.11_REPET

Optional: if you want to search for protein domain by HMM profiles in TE consensus, you need to have hmmpfam (from package hmmer2) or hmmpress and hmmscan (from package hmmer3) and an appropriate bank of HMM profiles ( http://hmmer.janelia.org/ ). It is advisable to use our last version is ProfilesBankForREPET_Pfam26.0_GypsyDB.hmm.tar.gz bank , specially formatted for REPET.

Developpement

The development of REPET follows eXtreme programming guidelines since the release 1.3 (in July 2009).

Contact

Reporting bugs or asking for features are much welcome! Please contact us via email at urgi-repet[[@]]versailles.inra.fr.

If you want to receive updates, send an email to urgi-repet[@]versailles.inra.fr with the following information:

  • First name
  • Last name
  • Email
  • Institution
  • Address
  • City
  • Zip
  • Country
  • Architecture ( linux-x64 )
  • Job scheduling system (SGE or Torque)

Authors and contributors

 Hadi Quesneville   Olivier Inizan
 Timothée Flutre  Claire Hoede
 Elodie Duprat   Sandie Arnoux
 Gaël Faroux  Françoise Alfama
 Delphine Autard  Jonathan Kreplak
 Timothée Chaumier  Véronique Jamilloux
 Marc Bras  Mark Moissette
Benoit Bely  Tinan Alaeitabar
Anna-Sophie Fiston-Lavier Emmanuelle Permal

  Funding

Access mode(s):

Downloadable

Keyword(s):

detection, annotation, transposable element, pipeline

Update: 09 Oct 2013
Creation date: 14 Oct 2011
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