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Mob DNA. 2015 Aug 4;6:13. doi: 10.1186/s13100-015-0044-6. eCollection 2015.

A call for benchmarking transposable element annotation methods.

Author information

1
School of Computer Science, McGill University, McConnell Engineering Bldg., Rm. 318, 3480 Rue University, Montréal, Québec H3A 0E9 Canada ; Department of Biology, McGill University, Stewart Biology Bldg., 1205 Ave. du Docteur-Penfield, Montréal, Québec H3A 1B1 Canada.
2
School of Computer Science, McGill University, McConnell Engineering Bldg., Rm. 318, 3480 Rue University, Montréal, Québec H3A 0E9 Canada ; McGill Centre for Bioinformatics, McGill University, Montréal, Québec Canada.
3
Department of Human Genetics, McGill University, Montréal, Québec Canada ; McGill University and Génome Québec Innovation Center, Montréal, Québec Canada.
4
Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain.
5
Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, 5 Rue Albert Turpin, 86073 Poitiers Cedex 9, France.
6
Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112 USA.
7
Institut des Sciences de l'Evolution de Montpellier (ISE-M), Equipe Evolution, Vecteurs, Adaptation et Symbiose, UMR5554 CNRS-Université Montpellier, Montpellier, 34090 cedex 05 France.
8
Laboratoire Evolution, Génomes, Comportement Ecologie, CNRS-Université Paris-Sud (UMR 9191)-IRD (UMR 247)-Université Paris-Saclay, F-91198 Gif-sur-Yvette, France.
9
Institute for Systems Biology, 401 Terry Ave. N, Seattle, WA 98109 USA.
10
Laboratoire Biometrie et Biologie Evolutive, Universite Claude Bernard-Lyon 1, UMR-CNRS 5558-Bat. Mendel, 43 bd du 11 novembre 1918, 69622 Villeurbanne cedex, France.
11
INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles, 78026 France.
12
University of Colorado School of Medicine, Aurora, CO 80045 USA.
13
Department of Computer Science, University of Montana, Missoula, MT 59812 USA.
14
Department of Biology, McGill University, Stewart Biology Bldg., 1205 Ave. du Docteur-Penfield, Montréal, Québec H3A 1B1 Canada.

Abstract

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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