Standardized benchmarking in the quest for orthologs

Abstract

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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Affiliated Institutions

• Laboratoire de Recherche en Informatique FR
• University of California, Berkeley US
• Science for Life Laboratory SE
• Center for Systems Biology US
• European Bioinformatics Institute GB
• SIB Swiss Institute of Bioinformatics CH
• Harvard University US
• European Molecular Biology Laboratory DE
• Lawrence Berkeley National Laboratory US
• University of Zurich CH
• Université Paris-Sud FR
• ETH Zurich CH
• University College London GB
• Institució Catalana de Recerca i Estudis Avançats ES
• Novo Nordisk Foundation DK
• Wellcome Trust GB
• Centre for Genomic Regulation ES
• Laboratoire d'Informatique de Paris-Nord FR
• University of Southern California US
• Université de Strasbourg FR
• Natural History Museum GB
• University of Copenhagen DK
• Stockholm University SE
• University of Lausanne CH

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