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PASTEClassifier

PASTEClassifier

PASTEClassifier


The PASTEClassifier (Pseudo Agent System for Transposable Elements Classification) is a transposable element (TE) classifier searching for structural features and similarity to classify TEs ( Hoede C. et al. 2014 ). It browses the whole spectrum of possible classifications at order level using Wicker hierarchical system ( Wicker T. et al., 2007 ). It is also able to automatically classify other repeated elements like SSR (Simple Sequence Repeats), rDNA or potential repeated host genes. The output is designed to facilitate manual curation by providing to the biologist all characteristics that have been found on each TE sequence.

Inputs are delimited sequences suspected to be TEs such as consensus sequences obtained by de novo TE detection softwares. For example, this sequence library could be built with the TEdenovo pipeline from the REPET package.

The PASTEClassifier package is distributed under the CeCILL license . Please read distributed LICENSE file.
It has been 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.

Before to use PASTEClassifier, read the tutorial

Prerequisites and installation notes are described in README

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[[@]]inra.fr.

Authors and contributors

Tina Alaeitabar Francoise Alfama
Sandie Arnoux Marc Bras
Laetitia Brigitte Timothee Chaumier
Johann Confais Timothee Flutre
Emeric Henrion Claire Hoede
Olivier Inizan Veronique Jamilloux
Jonathan Kreplak Nacer Mohellibi
Mark Moissette Erwan Ortie
Eric Penneçot Hadi Quesneville
Mariène Wan  

Funding

This work was supported by the grant TRANSNET (ANR-08-KBBE-012-02) from the french national research agency (ANR)


Access mode(s):

Downloadable

Keyword(s):

Transposable element; classification; Wicker classification; multi-agent classifier

Update: 16 Mar 2020
Creation date: 07 Oct 2013