Standardized benchmarking in the quest for orthologs.

Details

Serval ID
serval:BIB_E8F5620D5F4F
Type
Article: article from journal or magazin.
Collection
Publications
Title
Standardized benchmarking in the quest for orthologs.
Journal
Nature Methods
Author(s)
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., Jensen L.J., Martin M.J., Muffato M., Gabaldón T., Gabaldón T., Lewis S.E., Thomas P.D., Sonnhammer E., Dessimoz C.
Working group(s)
Quest for Orthologs consortium
Contributor(s)
Altenhoff AM., Boeckmann B., Capella-Gutierrez S., DeLuca T., Forslund K., Huerta-Cepas J., Linard B., Pereira C., Pryszcz LP., Schreiber F., da Silva AS. , Szklarczyk D., Train CM., Lecompte O., Xenarios I., Sjölander K., Martin MJ., Muffato M., Gabaldón T., Lewis SE., Thomas PD., Sonnhammer E., Dessimoz C.
ISSN
1548-7105 (Electronic)
ISSN-L
1548-7091
Publication state
Published
Issued date
2016
Peer-reviewed
Oui
Volume
13
Number
5
Pages
425-430
Language
english
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.
Pubmed
Web of science
Open Access
Yes
Create date
14/04/2016 16:31
Last modification date
20/08/2019 16:11
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