A call for benchmarking transposable element annotation methods
Hoen, Douglas R. (McGill University. Department of Biology)
Hickey, Glenn (McGill Centre for Bioinformatics)
Bourque, Guillaume (McGill University)
Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica)
Cordaux, Richard (Université de Poitiers)
Feschotte, Cédric (University of Utah. Department of Human Genetics)
Fiston-Lavier, Anna-Sophie (Institut des Sciences de l'Evolution de Montpellier)
Hua-Van, Aurélie (Université Paris-Saclay)
Hubley, Robert (Institute for Systems Biology)
Kapusta, Aurélie (University of Utah. Department of Human Genetics)
Lerat, Emmanuelle (Université Claude Bernard)
Maumus, Florian (INRA de Versailles-Grignon)
Pollock, David D. (University of Colorado)
Quesneville, Hadi (INRA de Versailles-Grignon)
Smit, Arian (Institute for Systems Biology)
Wheeler, Travis J. (University of Montana. Department of Computer Science)
Bureau, Thomas E. (McGill University. Department of Biology)
Blanchette, Mathieu (McGill Centre for Bioinformatics)

Data:	2015
Resum:	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.
Drets:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Llengua:	Anglès
Document:	Article ; recerca ; Versió publicada
Matèria:	Standard Benchmark ; Annotation Accuracy ; Probabilistic Annotation ; Simulated Genome ; Ongoing Genome Sequencing
Publicat a:	Mobile DNA, Vol. 6 (August 2015) , art. 13, ISSN 1759-8753

DOI: 10.1186/s13100-015-0044-6
PMID: 26244060

9 p, 588.8 KB

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