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Standardized benchmarking in the quest for orthologs.

  • Altenhoff AM Department of Computer Science, ETH Zurich, Zurich, Switzerland.
  • Boeckmann B Swiss-Prot Group, Swiss Institute of Bioinformatics, Geneva, Switzerland.
  • Capella-Gutierrez S Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
  • Dalquen DA Department of Genetics, Evolution, and Environment, University College London, London, UK.
  • DeLuca T Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA.
  • Forslund K Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
  • Huerta-Cepas J Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
  • Linard B Department of Life Sciences, Natural History Museum, London, UK.
  • Pereira C Université Paris-Sud, Laboratoire de Recherche en Informatique, Orsay, France.
  • Pryszcz LP Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
  • Schreiber F European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK.
  • da Silva AS European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK.
  • Szklarczyk D Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
  • Train CM Department of Computer Science, ETH Zurich, Zurich, Switzerland.
  • Bork P Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
  • Lecompte O LBGI, Computer Science Department, ICube, University of Strasbourg, Strasbourg, France.
  • von Mering C Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
  • Xenarios I Swiss-Prot Group, Swiss Institute of Bioinformatics, Geneva, Switzerland.
  • Sjölander K Department of Bioengineering, University of California, Berkeley, California, USA.
  • Jensen LJ The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
  • Martin MJ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK.
  • Muffato M European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK.
  • Gabaldón T Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
  • Lewis SE Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, California, USA.
  • Thomas PD Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Solna, Sweden.
  • Sonnhammer E Department of Genetics, Evolution, and Environment, University College London, London, UK.
  • Dessimoz C
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  • 2016-04-05
Published in:
  • Nature methods. - 2016
Archaea
Bacteria
Computational Biology
Databases, Genetic
Eukaryota
Gene Ontology
Genomics
Models, Genetic
Phylogeny
Proteomics
Sequence Analysis, Protein
Sequence Homology
Species Specificity
English 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.
Language
  • English
Open access status
hybrid
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Persistent URL
https://sonar.ch/global/documents/55126
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