3rd International Conference GIETE 2012, February 24-28 2012, Asilomar Pacific Grove, California, USA
24 Feb 2012 REPET V2: TEs detection and classification improvementsS Arnoux, V Jamilloux, T Chaumier, C Hoede, O Inizan, H Quesneville
The REPET package (Flutre et al, 2011) integrates two pipelines, which are constantly improving : TEdenovo and TEannot for transposable elements (TEs) detection and annotation. In the last release TEdenovo changed significantly.
The TEdenovo pipeline strategy is to find as much as possible potential TEs, and then to classify putative TEs in order to filter out false positives. The pipeline starts by the detection of repeated sequences comparing by alignments the genome with itself. These alignments are independently clustered according to different tools (RECON, GROUPER, PILER).Then, it builds multiple alignments from the clusters, from which a consensus sequence is derived. These consensus are classified according to TE features and redundancy is removed. Finally, there is the possibility to remove false-positives according to the classification (SSR, host genes, rDNA and under-represented unclassified consensus).
Two steps have been improved in REPET v2: