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Sökning: WFRF:(Capella Gutierrez Salvador) > Altenhoff Adrian M.

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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.
  • Altenhoff, Adrian M., et al. (författare)
  • The Quest for Orthologs benchmark service and consensus calls in 2020
  • 2020
  • Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 48:W1, s. W538-W545
  • Tidskriftsartikel (refereegranskat)abstract
    • The identification of orthologs-genes in different species which descended from the same gene in their last common ancestor-is a prerequisite for many analyses in comparative genomics and molecular evolution. Numerous algorithms and resources have been conceived to address this problem, but benchmarking and interpreting them is fraught with difficulties (need to compare them on a common input dataset, absence of ground truth, computational cost of calling orthologs). To address this, the Quest for Orthologs consortium maintains a reference set of proteomes and provides a web server for continuous orthology benchmarking (http://orthology.benchmarkservice.org). Furthermore, consensus ortholog calls derived from public benchmark submissions are provided on the Alliance of Genome Resources website, the joint portal of NIH-funded model organism databases.
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