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

Kristoffer Forslund 1 Cécile Pereira 2, 3, 4 Salvador Capella-Gutiérrez 5 Alan Sousa da Silva Adrian Altenhoff 6 Jaime Huerta-Cepas 7 Matthieu Muffato 8 Mateus Patricio Klaas Vandepoele 9 Ingo Ebersberger 10, 11 Judith Blake Jesualdo Tomás Fernández Breis Brigitte Boeckmann 6 Toni Gabaldon 7 Erik Sonnhammer 12 Christophe Dessimoz 13 Suzanna Lewis Carla Bello Sébastien Briois 14 Edward Chalstrey Hirokazu Chiba Oscar Conchillo-Solé Vincent Daubin 15 Todd Deluca 16 Jean-François Dufayard 17 Dannie Durand Jesualdo Tomás Fernández-Breis 18 Natasha Glover Alexander Hauser Davide Heller Mateus Kaduk Jan Koch Eugene Koonin 19 Evgenia Kriventseva 20 Shigehiro Kuraku 21 Odile Lecompte 22 Olivier Lespinet 23 Jeremy Levy Benjamin Liebeskind Benjamin Linard 24 Marc Marcet-Houben Martin Kauffmann Claire Mcwhite Sergei Mekhedov Sebastien Moretti 6 Steven Müller El-Mabrouk Nadia Cedric Notredame 25 Simon Penel 26 Ivana Pilizota Henning Redestig Marc Robinson-Rechavi 27 Fabian Schreiber 8 Kimmen Sjölander 28 Nives Škunca Martin Steinegger Damian Szklarczyk 29 Paul Thomas 30 Ernst Thuer Clément Train Ikuo Uchiyama Lucas Wittwer Ioannis Xenarios 31 Bethan Yates Evgeny Zdobnov 32 Robert Waterhouse
1 EMBL - European Molecular Biology Laboratory [Heidelberg]
2 University of Florida [Gainesville]
3 I2BC - Institut de Biologie Intégrative de la Cellule
4 BioInfo - LRI - Bioinformatique (LRI)
LRI - Laboratoire de Recherche en Informatique
5 Universitat Pompeu Fabra [Barcelona]
6 SIB - Swiss Institute of Bioinformatics [Lausanne]
7 CRG - Centre for Genomic Regulation
8 EMBL-EBI - European Bioinformatics Institute [Hinxton]
9 VIB Department of Plant Systems Biology
10 Senckenberg Climate and Research
11 Applied Bioinformatics
12 USC - University of Southern California
13 Department of Computer Science
14 LBCMCP - Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération
15 BPGE - Bioinformatique, phylogénie et génomique évolutive
PEGASE - Département PEGASE [LBBE]
16 HMS - Harvard Medical School [Boston]
17 UMR AGAP - Amélioration génétique et adaptation des plantes méditerranéennes et tropicales
18 Universidad de Murcia
19 NCBI - National Center for Biotechnology Information
20 University of Geneva Medical School
21 GRAS - Genome Resource and Analysis Unit
22 IGBMC - Institut de Génétique et de Biologie Moléculaire et Cellulaire
23 CNRS - Centre National de la Recherche Scientifique
24 MAB - Méthodes et Algorithmes pour la Bioinformatique
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
25 Comparative Bioinformatics
26 LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
27 Department of Ecology and Evolution
28 LBNL - Lawrence Berkeley National Laboratory [Berkeley]
29 UZH - Universität Zürich [Zürich]
30 Dstl - Defence Science and Technology Laboratory
31 SIB - Swiss Institute of Bioinformatics [Genève]
32 Medical School
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 orthol-ogy 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.
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https://hal.archives-ouvertes.fr/hal-01758841
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INRA | UNIV-LYON1 | MIPS | UNIV-MONTPELLIER | UMR8623 | CENTRALESUPELEC | SITE-ALSACE | JOLIOT | MONTPELLIER-SUPAGRO | UDL | LIRMM | CEA-DRF | UNIV-TLSE3 | I2BC | IGBMC | INRIA | CNRS | MAB | CIRAD | CEA-UPSAY | LRI-BIOINFO | AGROPOLIS | BIOENVIS | CEA | UNIV-PARIS-SACLAY | INRAE

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Kristoffer Forslund, Cécile Pereira, Salvador Capella-Gutiérrez, Alan Sousa da Silva, Adrian Altenhoff, et al.. Gearing up to handle the mosaic nature of life in the quest for orthologs. Bioinformatics, Oxford University Press (OUP), 2018, 34 (2), pp.323-329. ⟨10.1093/bioinformatics/btx542⟩. ⟨hal-01758841⟩

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