The recent successes of new sequencing technologies allow today sequencing increasingly large genomes at reduced costs. Transposable elements (TEs) constitute the most structurally dynamic components and the largest portion of nuclear sequences of these large genomes, e.g. 85% of the maize genome (Schnable et al. 2009), and 88% of the wheat genome (Choulet et al. 2010). Therefore, TEs annotation should be considered a major task in these genome projects.