Gearing up to handle the mosaic nature of life in the quest for orthologs

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• dc.contributor.author Forslund, Kristoffer
• dc.contributor.author Pereira, Cecile
• dc.contributor.author Capella Gutiérrez, Salvador Jesús, 1985-
• dc.contributor.author Sousa da Silva, Alan
• dc.contributor.author Altenhoff, Adrian M.
• dc.contributor.author Huerta Cepas, Jaime
• dc.contributor.author Muffato, Matthieu
• dc.contributor.author Patricio, Mateus
• dc.contributor.author Vandepoele, Klaas
• dc.contributor.author Ebersberger, Ingo
• dc.contributor.author Blake, Judith
• dc.contributor.author Fernández Breis, Jesualdo Tomás
• dc.contributor.author Quest for Orthologs consortium
• dc.contributor.author Boeckmann, Brigitte
• dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-
• dc.contributor.author Sonnhammer, Erik
• dc.contributor.author Dessimoz, Christophe
• dc.contributor.author Lewis, Suzanna E.
• dc.date.accessioned 2019-05-30T06:33:50Z
• dc.date.available 2019-05-30T06:33:50Z
• dc.date.issued 2018
• dc.description.abstract The Quest for Orthologs (QfO) is an open collaboration framework for experts in comparative phylogenomics and related research areas who have an interest in highly accurate orthology predictions and their applications. We here report highlights and discussion points from the QfO meeting 2015 held in Barcelona. Achievements in recent years have established a basis to support developments for improved orthology prediction and to explore new approaches. Central to the QfO effort is proper benchmarking of methods and services, as well as design of standardized datasets and standardized formats to allow sharing and comparison of results. Simultaneously, analysis pipelines have been improved, evaluated, and adapted to handle large datasets. All this would not have occurred without the long-term collaboration of Consortium members. Meeting regularly to review and coordinate complementary activities from a broad spectrum of innovative researchers clearly benefits the community. Highlights of the meeting include addressing sources of and legitimacy of disagreements between orthology calls, the context dependency of orthology definitions, special challenges encountered when analyzing very anciently rooted orthologies, orthology in the light of whole-genome duplications, and the concept of orthologous versus paralogous relationships at different levels, including domain-level orthology. Furthermore, particular needs for different applications (e.g. plant genomics, ancient gene families, and others) and the infrastructure for making orthology inferences available (e.g. interfaces with model organism databases) were discussed, with several ongoing efforts that are expected to be reported on during the upcoming 2017 QfO meeting.
• dc.description.sponsorship This work was supported by Spanish Ministry of Economy and Competitiveness grant BIO2012-37161 (to T.G.), Qatar National Research Fund NPRP 5-298-3-086 (to T.G.), European Research Council grant ERC-2012-StG-310325 (to T.G.), National Institutes of Health (NIH) grant R24 OD011883 (to S.E.L.), U41 HG002273 (to S.E.L. and P.D.T.), Swiss National Science Foundation grant PP00P3_150654 (to C.D.), UK Biotechnology and Biological Sciences Research Council grant BB/M015009/1 (to C.D.), Swiss State Secretariat for Education, Research and Innovation (SERI) funding (to B.B. and C.D.). M.M. and M.P. acknowledge support from the Wellcome Trust (grant number WT108749/Z/15/Z) and the European Molecular Biology Laboratory. The research leading to these results has received funding from the European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement n° 222664 (Quantomics).
• dc.format.mimetype application/pdf
• dc.identifier.citation Forslund K, Pereira C, Capella-Gutierrez S, Sousa da Silva A, Altenhoff A, Huerta-Cepas J, Muffato M, Patricio M, Vandepoele K, Ebersberger I, Blake J, Fernández Breis JT; Quest for Orthologs Consortium, Boeckmann B, Gabaldón T, Sonnhammer E, Dessimoz C, Lewis S. Gearing up to handle the mosaic nature of life in the quest for orthologs. Bioinformatics. 2018; 34(2):323-329. DOI: 10.1093/bioinformatics/btx542
• dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/btx542
• dc.identifier.issn 1367-4803
• dc.identifier.uri http://hdl.handle.net/10230/41659
• dc.language.iso eng
• dc.publisher Oxford University Press
• dc.relation.ispartof Bioinformatics. 2018; 34(2):323-329
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BIO2012-37161
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/222664
• dc.rights © The Author 2017. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.title Gearing up to handle the mosaic nature of life in the quest for orthologs
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion