title: LTRclassifier: A website for fast structural LTR retrotransposons classification in plants.
abstract: Automatic classification of LTR retrotransposons is a big challenge in the area of massive genomics. Many tools were developed to detect them but automatic classification is somehow challenging. Here we propose a simple approach,LTRclassifier, based onHMMrecognition followed byBLASTanalyses (i) to classify plant LTR retrotransposons in their respective superfamily, and (ii) to provide automatically a basic functional annotation of these elements. The method was tested on various TE databases, and shown to be robust and fast. This tool is available as a web service implemented at IRD bioinformatics facility, http://LTRclassifier.ird.fr/.
authors.affiliation: UMR DIADE IRD/UM, IRD , Montpellier Cedex 5 , France.
authors.forename: Cecile
authors.initials: C
authors.lastname: Monat
authors.affiliation: UMR DIADE IRD/UM, IRD , Montpellier Cedex 5 , France.
authors.forename: Ndomassi
authors.initials: N
authors.lastname: Tando
authors.affiliation: UMR DIADE IRD/UM, IRD , Montpellier Cedex 5 , France.
authors.forename: Christine
authors.initials: C
authors.lastname: Tranchant-Dubreuil
authors.affiliation: UMR DIADE IRD/UM, IRD , Montpellier Cedex 5 , France.
authors.forename: Francois
authors.initials: F
authors.lastname: Sabot
keywords: LTR retrotransposons; classification; superfamily