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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 REPET package


Its two main pipelines are dedicated to the detection, annotation and analysis of repeats in genomic sequences, specifically designed for transposable elements (TEs).

  •  TEdenovo: this pipeline starts by comparing the genome with itself using BLASTER. Then it cluster 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

 

Prerequisites

Proper usage of REPET requires a Unix-like system running on a cluster with the following, widely used components:

  • Python (v>=2.5) and its package MySQLdb;
  • MySQL (v>=5.0);
  • SGE (Sun Grid Engine) or Torque;
  • GNU awk (v>=3.1.5).

Moreover, external programs are also required:

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").

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 HMM profiles bank , specially formatted for REPET.

Download

You can obtain the latest public release of the REPET package by freely downloading the archive here .

The development of REPET follows eXtreme programming guidelines since the release 1.3 (in July 2009). The current release is the 2.0 (Wild Watermelon - February 2012).

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)

  Installation

First, download the compressed archive named "REPET_linux-x64_<version>.tar.gz". Then, decompress it with the command "tar -xvzf REPET_linux-x64_<version>.tar.gz", to obtain the package in a new directory "REPET_linux-x64_<version>". In this new directory, you will find some documentation, especially a README, a FAQ and tutorials in the subdirectory "doc/".

The C++ programs for BLASTER, GROUPER and MATCHER are given as binaries and the rest of the REPET package is composed of Python programs. Thus, you don't need to compile anything and the installation is straightforward.

Contact

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

Authors and contributors

 Hadi Quesneville  Benoit Bely
 Timothée Flutre  Olivier Inizan
 Elodie Duprat  Claire Hoede
 Gaël Faroux  Françoise Alfama
 Delphine Autard  Sandie Arnoux
 Timothée Chaumier  Véronique Jamilloux
 Marc Bras  Mark Moissette

  Funding

Access mode(s):

Downloadable

Keyword(s):

detection, annotation, transposable element

Update: 18 Mar 2013
Creation date: 14 Oct 2011
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