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