Standardized benchmarking in the quest for orthologs

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Standardized benchmarking in the quest for orthologs. / Altenhoff, Adrian M; Boeckmann, Brigitte; Capella-Gutierrez, Salvador; Dalquen, Daniel A; DeLuca, Todd; Forslund, Kristoffer; Huerta-Cepas, Jaime; Linard, Benjamin; Pereira, Cécile; Pryszcz, Leszek P; Schreiber, Fabian; da Silva, Alan Sousa; Szklarczyk, Damian; Train, Clément-Marie; Bork, Peer; Lecompte, Odile; von Mering, Christian; Xenarios, Ioannis; Sjölander, Kimmen; Jensen, Lars Juhl; Martin, Maria J; Muffato, Matthieu; Gabaldón, Toni; Lewis, Suzanna E; Thomas, Paul D; Sonnhammer, Erik; Dessimoz, Christophe; Quest for Orthologs consortium.

In: Nature Methods, Vol. 13, 05.2016, p. 425-30.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

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, C-M, 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 & Quest for Orthologs consortium 2016, 'Standardized benchmarking in the quest for orthologs', Nature Methods, vol. 13, pp. 425-30. https://doi.org/10.1038/nmeth.3830

APA

Altenhoff, A. M., Boeckmann, B., Capella-Gutierrez, S., Dalquen, D. A., DeLuca, T., Forslund, K., Huerta-Cepas, J., Linard, B., Pereira, C., Pryszcz, L. P., Schreiber, F., da Silva, A. S., Szklarczyk, D., Train, C-M., Bork, P., Lecompte, O., von Mering, C., Xenarios, I., Sjölander, K., ... Quest for Orthologs consortium (2016). Standardized benchmarking in the quest for orthologs. Nature Methods, 13, 425-30. https://doi.org/10.1038/nmeth.3830

Vancouver

Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K et al. Standardized benchmarking in the quest for orthologs. Nature Methods. 2016 May;13:425-30. https://doi.org/10.1038/nmeth.3830

Author

Altenhoff, Adrian M ; Boeckmann, Brigitte ; Capella-Gutierrez, Salvador ; Dalquen, Daniel A ; DeLuca, Todd ; Forslund, Kristoffer ; Huerta-Cepas, Jaime ; Linard, Benjamin ; Pereira, Cécile ; Pryszcz, Leszek P ; Schreiber, Fabian ; da Silva, Alan Sousa ; Szklarczyk, Damian ; Train, Clément-Marie ; Bork, Peer ; Lecompte, Odile ; von Mering, Christian ; Xenarios, Ioannis ; Sjölander, Kimmen ; Jensen, Lars Juhl ; Martin, Maria J ; Muffato, Matthieu ; Gabaldón, Toni ; Lewis, Suzanna E ; Thomas, Paul D ; Sonnhammer, Erik ; Dessimoz, Christophe ; Quest for Orthologs consortium. / Standardized benchmarking in the quest for orthologs. In: Nature Methods. 2016 ; Vol. 13. pp. 425-30.

Bibtex

@article{e53d425a57064680861970df25ac6c39,

title = "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.",

author = "Altenhoff, {Adrian M} and Brigitte Boeckmann and Salvador Capella-Gutierrez and Dalquen, {Daniel A} and Todd DeLuca and Kristoffer Forslund and Jaime Huerta-Cepas and Benjamin Linard and C{\'e}cile Pereira and Pryszcz, {Leszek P} and Fabian Schreiber and {da Silva}, {Alan Sousa} and Damian Szklarczyk and Cl{\'e}ment-Marie Train and Peer Bork and Odile Lecompte and {von Mering}, Christian and Ioannis Xenarios and Kimmen Sj{\"o}lander and Jensen, {Lars Juhl} and Martin, {Maria J} and Matthieu Muffato and Toni Gabald{\'o}n and Lewis, {Suzanna E} and Thomas, {Paul D} and Erik Sonnhammer and Christophe Dessimoz and {Quest for Orthologs consortium}",

note = "AR2016",

year = "2016",

month = may,

doi = "10.1038/nmeth.3830",

language = "English",

volume = "13",

pages = "425--30",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "nature publishing group",

}

RIS

TY - JOUR

T1 - Standardized benchmarking in the quest for orthologs

AU - Altenhoff, Adrian M

AU - Boeckmann, Brigitte

AU - Capella-Gutierrez, Salvador

AU - Dalquen, Daniel A

AU - DeLuca, Todd

AU - Forslund, Kristoffer

AU - Huerta-Cepas, Jaime

AU - Linard, Benjamin

AU - Pereira, Cécile

AU - Pryszcz, Leszek P

AU - Schreiber, Fabian

AU - da Silva, Alan Sousa

AU - Szklarczyk, Damian

AU - Train, Clément-Marie

AU - Bork, Peer

AU - Lecompte, Odile

AU - von Mering, Christian

AU - Xenarios, Ioannis

AU - Sjölander, Kimmen

AU - Jensen, Lars Juhl

AU - Martin, Maria J

AU - Muffato, Matthieu

AU - Gabaldón, Toni

AU - Lewis, Suzanna E

AU - Thomas, Paul D

AU - Sonnhammer, Erik

AU - Dessimoz, Christophe

AU - Quest for Orthologs consortium

N1 - AR2016

PY - 2016/5

Y1 - 2016/5

N2 - 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.

AB - 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.

U2 - 10.1038/nmeth.3830

DO - 10.1038/nmeth.3830

M3 - Journal article

C2 - 27043882

VL - 13

SP - 425

EP - 430

JO - Nature Methods

JF - Nature Methods

SN - 1548-7091

ER -

ID: 160131438