New developments for the Quest for Orthologs benchmark service.

Autor:	Altenhoff A; ETH Zurich, Department of Computer Science,Universitätstrasse 19, 8092 Zurich, Switzerland.; SIB Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, 1015 Lausanne, Switzerland., Nevers Y; SIB Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, 1015 Lausanne, Switzerland.; Department of Computational Biology, University of Lausanne, Génopode, 1015 Lausanne, Switzerland., Tran V; Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Department of Biosciences, Goethe University, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany., Jyothi D; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK., Martin M; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK., Cosentino S; Department of Integrated Biosciences, University of Tokyo, Tokyo 277-0882, Japan., Majidian S; SIB Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, 1015 Lausanne, Switzerland.; Department of Computational Biology, University of Lausanne, Génopode, 1015 Lausanne, Switzerland., Marcet-Houben M; Barcelona Supercomputing Center (BSC-CNS), Plaça d'Eusebi Güell, 1-3, 08034 Barcelona, Spain.; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer Baldiri Reixac, 10, 08028 Barcelona, Spain.; CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Monforte de Lemos, 3-5. Pabellón 11, 28029 Madrid, Spain., Fuentes-Palacios D; Barcelona Supercomputing Center (BSC-CNS), Plaça d'Eusebi Güell, 1-3, 08034 Barcelona, Spain.; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer Baldiri Reixac, 10, 08028 Barcelona, Spain., Persson E; Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden., Walsh T; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire CB10 1SD, UK., Lecompte O; Department of Computer Science, ICube, UMR 7357, Centre de Recherche en Biomédecine de Strasbourg, University of Strasbourg, CNRS, 1 rue Eugène Boeckel, 67000, Strasbourg, France., Gabaldón T; Barcelona Supercomputing Center (BSC-CNS), Plaça d'Eusebi Güell, 1-3, 08034 Barcelona, Spain.; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Carrer Baldiri Reixac, 10, 08028 Barcelona, Spain.; CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Monforte de Lemos, 3-5. Pabellón 11, 28029 Madrid, Spain.; Catalan Institution for Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08003 Barcelona, Spain., Kelly S; Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK., Hu Y; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA., Iwasaki W; Department of Integrated Biosciences, University of Tokyo, Tokyo 277-0882, Japan., Capella-Gutierrez S; Barcelona Supercomputing Center (BSC-CNS), Plaça d'Eusebi Güell, 1-3, 08034 Barcelona, Spain., Dessimoz C; SIB Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, 1015 Lausanne, Switzerland.; Department of Computational Biology, University of Lausanne, Génopode, 1015 Lausanne, Switzerland., Thomas PD; Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90033, USA., Ebersberger I; Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Department of Biosciences, Goethe University, Max-von-Laue-Str. 13, D-60438 Frankfurt, Germany.; Senckenberg Biodiversity and Climate Research Centre (S-BIK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.; LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany., Sonnhammer E; Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden.
Jazyk:	angličtina
Zdroj:	NAR genomics and bioinformatics [NAR Genom Bioinform] 2024 Dec 11; Vol. 6 (4), pp. lqae167. Date of Electronic Publication: 2024 Dec 11 (Print Publication: 2024).
DOI:	10.1093/nargab/lqae167
Abstrakt:	The Quest for Orthologs (QfO) orthology benchmark service (https://orthology.benchmarkservice.org) hosts a wide range of standardized benchmarks for orthology inference evaluation. It is supported and maintained by the QfO consortium, and is used to gather ortholog predictions and to examine strengths and weaknesses of newly developed and existing orthology inference methods. The web server allows different inference methods to be compared in a standardized way using the same proteome data. The benchmark results are useful for developing new methods and can help researchers to guide their choice of orthology method for applications in comparative genomics and phylogenetic analysis. We here present a new release of the Orthology Benchmark Service with a new benchmark based on feature architecture similarity as well as updated reference proteomes. We further provide a meta-analysis of the public predictions from 18 different orthology assignment methods to reveal how they relate in terms of ortholog predictions and benchmark performance. These results can guide users of orthologs to the best suited method for their purpose. (© The Author(s) 2024. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.)
Databáze:	MEDLINE
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