Contributors: Swiss Institute of Bioinformatics Lausanne (SIB); Université de Lausanne = University of Lausanne (UNIL); Universitat Pompeu Fabra Barcelona (UPF); Department of Genetics, Evolution and Environment; University College of London London (UCL); Harvard Medical School Boston (HMS); European Molecular Biology Laboratory Heidelberg (EMBL); Méthodes et Algorithmes pour la Bioinformatique (MAB); Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM); Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS); Laboratoire de Recherche en Informatique (LRI); Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS); Barcelona Institute of Science and Technology (BIST); European Bioinformatics Institute Hinxton (EMBL-EBI); EMBL Heidelberg; Universität Zürich Zürich = University of Zurich (UZH); Department of Computer Science ETH Zürich (D-INFK); Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology Zürich (ETH Zürich); Max Delbrück Centre for Molecular Medicine; Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC); Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS); Swiss Institute of Bioinformatics Genève (SIB); Lawrence Berkeley National Laboratory Berkeley (LBNL); Novo Nordisk Foundation Center for Protein Research (CPR); Faculty of Health and Medical Sciences; University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH); SRI International, Evolutionary System Biolology; University of Southern California (USC); Department of Computer Science; This work was supported by Swiss National Science Foundation grant PP00P3_150654 (to C.D.), UK Biotechnology and Biological Sciences Research Council grant BB/L018241/1 (to C.D.), Spanish Ministry of Economy and Competitiveness grant BIO2012-37161 (to T.G.), Qatar National Research Fund NPRP 5-298-3-086 (to T.G.), European Research Council grant ERC-2012-StG-310325 (to T.G.), National Institutes of Health (NIH) grantR24 OD011883 (to S.E.L.), U41 HG002273 (to S.E.L. and P.D.T.), U41 HG007822 (to M.J.M. and I.X.), Swiss State Secretariat for Education, Research and Innovation (SERI) funding (to I.X. and C.D.), US National Science Foundation EAGER Award #1355632 (to K.S.) and ANR project BIP-BIP ANR-10-BINF-03-02 (to O.L.). Furthermore, A.S.d.S., J.H.-C., M.J.M., M.M. and P.B. acknowledge support from the European Molecular Biology Laboratory, M.M. acknowledges support from the Wellcome Trust (WT095908), S.E.L. acknowledges support from Lawrence Berkeley National Laboratory core funds (Office of Basic Energy Sciences and US Department of Energy Contract No. DE-AC02-05CH11231), L.J.J. acknowledges support from the Novo Nordisk Foundation (Grant No. NNF14CC0001) and L.P.P. acknowledges support from the La Caixa–CRG International Fellowship Program.; ANR-10-BINF-0003,Bip:Bip,Paradigme d'inference bayesienne pour la Biologie structurale in silico(2010)
نبذة مختصرة : International audience ; 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.
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