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Standardized benchm...
Standardized benchmarking in the quest for orthologs
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Altenhoff, Adrian M. (author)
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Boeckmann, Brigitte (author)
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Capella-Gutierrez, Salvador (author)
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Dalquen, Daniel A. (author)
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DeLuca, Todd (author)
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Forslund, Kristoffer (author)
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Huerta-Cepas, Jaime (author)
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Linard, Benjamin (author)
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Pereira, Cecile (author)
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Pryszcz, Leszek P. (author)
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Schreiber, Fabian (author)
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da Silva, Alan Sousa (author)
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Szklarczyk, Damian (author)
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Train, Clement-Marie (author)
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Bork, Peer (author)
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Lecompte, Odile (author)
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von Mering, Christian (author)
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Xenarios, Ioannis (author)
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Sjölander, Kimmen (author)
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Juhl Jensen, Lars (author)
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Martin, Maria J. (author)
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Muffato, Matthieu (author)
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Gabaldon, Toni (author)
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Lewis, Suzanna E. (author)
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Thomas, Paul D. (author)
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- Sonnhammer, Erik (author)
- Stockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab)
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Dessimoz, Christophe (author)
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(creator_code:org_t)
- 2016
- 2016
- English.
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In: Nature Methods. - 1548-7091 .- 1548-7105. ; 13:5, s. 425-
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https://doi.org/10.1...
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Abstract
Subject headings
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- 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.
Subject headings
- NATURVETENSKAP -- Biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences (hsv//eng)
Publication and Content Type
- ref (subject category)
- art (subject category)
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- By the author/editor
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Altenhoff, Adria ...
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Boeckmann, Brigi ...
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Capella-Gutierre ...
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Dalquen, Daniel ...
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DeLuca, Todd
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Forslund, Kristo ...
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show more...
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Huerta-Cepas, Ja ...
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Linard, Benjamin
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Pereira, Cecile
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Pryszcz, Leszek ...
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Schreiber, Fabia ...
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da Silva, Alan S ...
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Szklarczyk, Dami ...
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Train, Clement-M ...
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Bork, Peer
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Lecompte, Odile
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von Mering, Chri ...
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Xenarios, Ioanni ...
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Sjölander, Kimme ...
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Juhl Jensen, Lar ...
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Martin, Maria J.
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Muffato, Matthie ...
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Gabaldon, Toni
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Lewis, Suzanna E ...
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Thomas, Paul D.
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Sonnhammer, Erik
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Dessimoz, Christ ...
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show less...
- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
- Articles in the publication
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Nature Methods
- By the university
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Stockholm University