A call for benchmarking transposable element annotation methods. - Archive ouverte HAL Access content directly
Journal Articles Mobile DNA Year : 2014

A call for benchmarking transposable element annotation methods.

Douglas R Hoen
  • Function : Author
Glenn Hickey
  • Function : Author
Guillaume Bourque
  • Function : Author
Josep Casacuberta
Cédric Feschotte
  • Function : Author
Anna-Sophie Fiston-Lavier
  • Function : Author
Aurélie Hua-Van
Robert Hubley
  • Function : Author
Aurélie Kapusta
  • Function : Author
Florian Maumus
David D Pollock
  • Function : Author
Hadi Quesneville
Arian Smit
  • Function : Author
Travis J Wheeler
  • Function : Author
Thomas E Bureau
  • Function : Author
Mathieu Blanchette
  • Function : Author


DNA derived from transposable elements (TEs) constitutes large parts of the genomes of complex eukaryotes, with major impacts not only on genomic research but also on how organisms evolve and function. Although a variety of methods and tools have been developed to detect and annotate TEs, there are as yet no standard benchmarks-that is, no standard way to measure or compare their accuracy. This lack of accuracy assessment calls into question conclusions from a wide range of research that depends explicitly or implicitly on TE annotation. In the absence of standard benchmarks, toolmakers are impeded in improving their tools, annotators cannot properly assess which tools might best suit their needs, and downstream researchers cannot judge how accuracy limitations might impact their studies. We therefore propose that the TE research community create and adopt standard TE annotation benchmarks, and we call for other researchers to join the authors in making this long-overdue effort a success.
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hal-01204840 , version 1 (28-05-2020)



Douglas R Hoen, Glenn Hickey, Guillaume Bourque, Josep Casacuberta, Richard Cordaux, et al.. A call for benchmarking transposable element annotation methods.. Mobile DNA, 2014, 6, pp.13. ⟨10.1186/s13100-015-0044-6⟩. ⟨hal-01204840⟩
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