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Standardized benchmarking in the quest for orthologs

Altenhoff, AM; Boeckmann, B; Capella-Gutierrez, S; Dalquen, DA; DeLuca, T; Forslund, K; Huerta-Cepas, J; ... Dessimoz, C; + view all (2016) Standardized benchmarking in the quest for orthologs. Nature Methods , 13 (5) pp. 425-430. 10.1038/nmeth.3830. Green open access

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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.

Type: Article
Title: Standardized benchmarking in the quest for orthologs
Open access status: An open access version is available from UCL Discovery
DOI: 10.1038/nmeth.3830
Publisher version: http://doi.org/10.1038/nmeth.3830
Language: English
Additional information: This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/.
Keywords: Phylogeny, Protein function predictions, Sequence annotation, Standards
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: http://discovery.ucl.ac.uk/id/eprint/1478137
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