Fiche publication
Date publication
mai 2016
Journal
Nature methods
Auteurs
Membres identifiés du Cancéropôle Est :
Pr LECOMPTE Odile
Tous les auteurs :
Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M, ,Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C
Lien Pubmed
Résumé
Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is generally unknown and orthologs are used for very different applications across phyla, requiring different precision-recall trade-offs. As a result, it is difficult to assess the performance of orthology inference methods. Here, we present a community effort to establish standards and an automated web-based service to facilitate orthology benchmarking. Using this service, we characterize 15 well-established inference methods and resources on a battery of 20 different benchmarks. Standardized benchmarking provides a way for users to identify the most effective methods for the problem at hand, sets a minimum requirement for new tools and resources, and guides the development of more accurate orthology inference methods.
Mots clés
Archaea, classification, Bacteria, classification, Computational Biology, methods, Databases, Genetic, Eukaryota, classification, Gene Ontology, Genomics, methods, Models, Genetic, Phylogeny, Proteomics, methods, Sequence Analysis, Protein, Sequence Homology, Species Specificity
Référence
Nat Methods. 2016 05;13(5):425-30
