International,  COM (talks)

ALPHY (Alignement, Phylogénie, Génomique Comparative et Bioinformatique), Lyon, 6-7 février 2013

07 Feb 2013   Scouting and scraping the A. thaliana repeatome

Maumus F., Quesneville H.

Arabidopsis thaliana is a model plant species. Annotation of repeats and repeat‐derived sequences (collectively referred to as the repeatome) is crucial for understanding genome composition. A variety of de novo repeat identification programs are available that are based on the search of k-mers, homologies, or structures. We have combined a compilation of programs that enabled to substantially improve the detection of the A. thaliana repeatome. We also describe the results from attempts to reveal deeper layers of the repeatome using a series of new approaches. After learning from our in silico experiments, we propose a deep, compendium annotation of the A. thaliana repeatome that may help understanding genome evolution as well as transcriptional and epigenetic controls.