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Träfflista för sökning "WFRF:(Gabaldon Toni) ;pers:(Martín María J.)"

Sökning: WFRF:(Gabaldon Toni) > Martín María J.

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1.
  • Altenhoff, Adrian M., et al. (författare)
  • Standardized benchmarking in the quest for orthologs
  • 2016
  • Ingår i: Nature Methods. - 1548-7091 .- 1548-7105. ; 13:5, s. 425-
  • Tidskriftsartikel (refereegranskat)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.
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2.
  • Nevers, Yannis, et al. (författare)
  • The Quest for Orthologs orthology benchmark service in 2022
  • 2022
  • Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 50:W1, s. W623-W632
  • Tidskriftsartikel (refereegranskat)abstract
    • The Orthology Benchmark Service (https://orthology.benchmarkservice.org) is the gold standard for orthology inference evaluation, supported and maintained by the Quest for Orthologs consortium. It is an essential resource to compare existing and new methods of orthology inference (the bedrock for many comparative genomics and phylogenetic analysis) over a standard dataset and through common procedures. The Quest for Orthologs Consortium is dedicated to maintaining the resource up to date, through regular updates of the Reference Proteomes and increasingly accessible data through the OpenEBench platform. For this update, we have added a new benchmark based on curated orthology assertion from the Vertebrate Gene Nomenclature Committee, and provided an example meta-analysis of the public predictions present on the platform.
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