2013
ALPHY (Alignement, Phylogénie, Génomique Comparative et Bioinformatique), Lyon, 6-7 février 2013
07 Feb 2013 Scouting and scraping the A. thaliana repeatomeMaumus 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.
Creation date: 05 Jul 2013
eZ PublishPublication supervisor: A-F. Adam-Blondon
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