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Bioinformatics. 2017 Aug 30. doi: 10.1093/bioinformatics/btx542. [Epub ahead of print]

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

Author information

1
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
2
Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida at Gainesville, Gainesville, FL, USA.
3
Institute for Integrative Biology of the Cell (I2BC), Laboratoire de Recherche en Informatique (LRI), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
4
Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
5
Spanish National Bioinformatics Institute (INB), Spanish National Cancer Research Centre, Madrid, Spain.
6
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK.
7
Dept. of Computer Science, ETH Zurich, Zurich, Switzerland.
8
Computational Biochemistry Research Group, Swiss Institute of Bioinformatics (SIB), Zurich, Switzerland.
9
Center for Plant Systems Biology, VIB & Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
10
Applied Bioinformatics, Goethe-Universitet Frankfurt, Frankfurt, Germany.
11
Senckenberg Climate and Research Center Frankfurt (BIK-F), Frankfurt, Germany.
12
Jackson Laboratory, Bar Harbor, ME, USA.
13
University of Murcia, Murcia, Spain.
14
Swiss-Prot Group, Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland.
15
Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
16
Universitat Pompeu Fabra (UPF), Barcelona, Spain.
17
Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain.
18
Stockholm Bioinformatics Center, Dept. of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Solna, Sweden.
19
Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
20
Dept. of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
21
Dept. of Genetics, Evolution, and Environment, University College London, UK.
22
Dept. Computer Science, University College London, UK.
23
Swiss Institute of Bioinformatics, Lausanne, Switzerland.
24
Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA.

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.

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