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Standardized benchmarking in the quest for orthologs

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Item Type:Article
Title:Standardized benchmarking in the quest for orthologs
Creators Name:Altenhoff, A.M. and Boeckmann, B. and Capella-Gutierrez, S. and Dalquen, D.A. and DeLuca, T. and Forslund, K. and Huerta-Cepas, J. and Linard, B. and Pereira, C. and Pryszcz, L.P. and Schreiber, F. and da Silva, A.S. and Szklarczyk, D. and Train, C.M. and Bork, P. and Lecompte, O. and von Mering, C. and Xenarios, I. and Sjoelander, K. and Jensen, L.J. and Martin, M.J. and Muffato, M. and Gabaldon, T. and Lewis, S.E. and Thomas, P.D. and Sonnhammer, E. and Dessimoz, C.
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.
Keywords:Archaea, Bacteria, Computational Biology, Eukaryota, Gene Ontology, Genetic Databases, Genetic Models, Genomics, Phylogeny, Protein Sequence Analysis, Proteomics, Sequence Homology, Species Specificity
Source:Nature Methods
ISSN:1548-7091
Publisher:Nature Publishing Group (U.S.A.)
Volume:13
Number:5
Page Range:425-430
Date:May 2016
Official Publication:https://doi.org/10.1038/nmeth.3830
PubMed:View item in PubMed

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