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).
Repet v2.2 package also contains:
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").
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.
The development of REPET follows eXtreme programming guidelines since the release 1.3 (in July 2009).
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:
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||Tina Alaeitabar|
|Anna-Sophie Fiston-Lavier||Emmanuelle Permal|