The Quest for Orthologs benchmark service and consensus calls in 2020-Reference-Cited by-同舟云学术

The Quest for Orthologs benchmark service and consensus calls in 2020

Published:2020-05-06 Issue:W1 Volume:48 Page:W538-W545
ISSN:0305-1048
Container-title:Nucleic Acids Research
language:en
Short-container-title:

Author:

Altenhoff Adrian M¹²^ORCID,Garrayo-Ventas Javier³^ORCID,Cosentino Salvatore⁴^ORCID,Emms David⁵^ORCID,Glover Natasha M¹⁶⁷^ORCID,Hernández-Plaza Ana⁸,Nevers Yannis¹⁶⁷⁹^ORCID,Sundesha Vicky³^ORCID,Szklarczyk Damian¹¹⁰,Fernández José M³^ORCID,Codó Laia³^ORCID,for Orthologs Consortium the Quest,Gelpi Josep Ll³¹¹^ORCID,Huerta-Cepas Jaime⁸^ORCID,Iwasaki Wataru⁴^ORCID,Kelly Steven⁵^ORCID,Lecompte Odile⁹^ORCID,Muffato Matthieu¹²^ORCID,Martin Maria J¹²^ORCID,Capella-Gutierrez Salvador³^ORCID,Thomas Paul D¹³^ORCID,Sonnhammer Erik¹⁴^ORCID,Dessimoz Christophe¹⁶⁷¹⁵¹⁶^ORCID

Affiliation:

1. SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland

2. ETH Zurich, Department of Computer Science, Zurich, Switzerland

3. Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain

4. Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan

5. Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, UK

6. Department of Computational Biology, University of Lausanne, Lausanne, Switzerland

7. Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland

8. Centro de Biotecnologia y Genomica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, 28223, Pozuelo de Alarcón, Madrid, Spain

9. Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France

10. Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland

11. Department of Biochemistry and Molecular Biomedicine. University of Barcelona. Barcelona, Spain

12. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK

13. Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, USA

14. Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden

15. Department of Genetics, Evolution & Environment, University College London, London, UK

16. Department of Computer Science, University College London, London, UK

Abstract

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.

Funder

Swiss Institute of Bioinformatics

NSF

NIH NHGRI

INB

H2020 ELIXIR-EXCELERATE

Ministerio de Ciencia, Innovación y Universidades

Horizon 2020 - Research and Innovation Framework Programme

Consejería de Educación, Juventud y Deporte de la Comunidad de Madrid

National Institutes of Health

European Molecular Biology Laboratory

Wellcome Trust