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Mob Genet Elements. 2016 Sep 26;6(6):e1241050. doi: 10.1080/2159256X.2016.1241050. eCollection 2016.

LTRclassifier: A website for fast structural LTR retrotransposons classification in plants.

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1
UMR DIADE IRD/UM, IRD , Montpellier Cedex 5 , France.

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 on HMM recognition followed by BLAST analyses (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/.

KEYWORDS:

LTR retrotransposons; classification; superfamily

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