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The Quest for Orthologs orthology benchmark service in 2022.
Nevers, Yannis; Jones, Tamsin E M; Jyothi, Dushyanth; Yates, Bethan; Ferret, Meritxell; Portell-Silva, Laura; Codo, Laia; Cosentino, Salvatore; Marcet-Houben, Marina; Vlasova, Anna; Poidevin, Laetitia; Kress, Arnaud; Hickman, Mark; Persson, Emma; Pilizota, Ivana; Guijarro-Clarke, Cristina; Iwasaki, Wataru; Lecompte, Odile; Sonnhammer, Erik; Roos, David S; Gabaldón, Toni; Thybert, David; Thomas, Paul D; Hu, Yanhui; Emms, David M; Bruford, Elspeth; Capella-Gutierrez, Salvador; Martin, Maria J; Dessimoz, Christophe; Altenhoff, Adrian.
Afiliação
  • Nevers Y; Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
  • Jones TEM; Swiss Institute for Bioinformatics, University of Lausanne, Lausanne, Switzerland.
  • Jyothi D; HUGO Gene Nomenclature Committee (HGNC), European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
  • Yates B; Protein Function development, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
  • Ferret M; HUGO Gene Nomenclature Committee (HGNC), European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
  • Portell-Silva L; Barcelona Supercomputing Centre (BSC-CNS). Plaça Eusebi Güell, 1-3 08034 Barcelona, Spain.
  • Codo L; Barcelona Supercomputing Centre (BSC-CNS). Plaça Eusebi Güell, 1-3 08034 Barcelona, Spain.
  • Cosentino S; Barcelona Supercomputing Centre (BSC-CNS). Plaça Eusebi Güell, 1-3 08034 Barcelona, Spain.
  • Marcet-Houben M; Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Tokyo, Japan.
  • Vlasova A; Barcelona Supercomputing Centre (BSC-CNS). Plaça Eusebi Güell, 1-3 08034 Barcelona, Spain.
  • Poidevin L; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.
  • Kress A; Barcelona Supercomputing Centre (BSC-CNS). Plaça Eusebi Güell, 1-3 08034 Barcelona, Spain.
  • Hickman M; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.
  • Persson E; Department of Computer Science, ICube, UMR 7357, Centre de Recherche en Biomédecine de Strasbourg, University of Strasbourg, CNRS, Strasbourg, France.
  • Pilizota I; BiGEst-ICube Platform, ICube, UMR 7357, Centre de Recherche en Biomédecine de Strasbourg, University of Strasbourg, CNRS, Strasbourg, France.
  • Guijarro-Clarke C; Department of Computer Science, ICube, UMR 7357, Centre de Recherche en Biomédecine de Strasbourg, University of Strasbourg, CNRS, Strasbourg, France.
  • Iwasaki W; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
  • Lecompte O; Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.
  • Sonnhammer E; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
  • Roos DS; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
  • Thybert D; Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Tokyo, Japan.
  • Thomas PD; Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Japan.
  • Hu Y; Department of Computer Science, ICube, UMR 7357, Centre de Recherche en Biomédecine de Strasbourg, University of Strasbourg, CNRS, Strasbourg, France.
  • Emms DM; Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.
  • Bruford E; Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
  • Capella-Gutierrez S; Barcelona Supercomputing Centre (BSC-CNS). Plaça Eusebi Güell, 1-3 08034 Barcelona, Spain.
  • Martin MJ; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.
  • Dessimoz C; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
  • Altenhoff A; Centro de Investigaciones Biomédicas en Red de Enfermedades Infecciosas, Barcelona, Spain.
Nucleic Acids Res ; 50(W1): W623-W632, 2022 07 05.
Article em En | MEDLINE | ID: mdl-35552456
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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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Benchmarking / Genômica Tipo de estudo: Systematic_reviews Idioma: En Revista: Nucleic Acids Res Ano de publicação: 2022 Tipo de documento: Article País de afiliação: Suíça
Texto completo
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Benchmarking / Genômica Tipo de estudo: Systematic_reviews Idioma: En Revista: Nucleic Acids Res Ano de publicação: 2022 Tipo de documento: Article País de afiliação: Suíça