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

(2018) BIOINFORMATICS. 34(2). p.323-329
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Bioinformatics: from nucleotids to networks (N2N)
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.
Keywords
FUNCTIONAL ANNOTATIONS, SEQUENCE, TREE

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Citation

Please use this url to cite or link to this publication:

Chicago
Forslund, Kristoffer, Cecile Pereira, Salvador Capella-Gutierrez, Alan Sousa da Silva, Adrian Altenhoff, Jaime Huerta-Cepas, Matthieu Muffato, et al. 2018. “Gearing up to Handle the Mosaic Nature of Life in the Quest for Orthologs.” Bioinformatics 34 (2): 323–329.
APA
Forslund, K., Pereira, C., Capella-Gutierrez, S., Sousa da Silva, A., Altenhoff, A., Huerta-Cepas, J., Muffato, M., et al. (2018). Gearing up to handle the mosaic nature of life in the quest for orthologs. BIOINFORMATICS, 34(2), 323–329.
Vancouver
1.
Forslund K, Pereira C, Capella-Gutierrez S, Sousa da Silva A, Altenhoff A, Huerta-Cepas J, et al. Gearing up to handle the mosaic nature of life in the quest for orthologs. BIOINFORMATICS. 2018;34(2):323–9.
MLA
Forslund, Kristoffer, Cecile Pereira, Salvador Capella-Gutierrez, et al. “Gearing up to Handle the Mosaic Nature of Life in the Quest for Orthologs.” BIOINFORMATICS 34.2 (2018): 323–329. Print.
@article{8558082,
  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.},
  author       = {Forslund, Kristoffer and Pereira, Cecile and Capella-Gutierrez, Salvador and Sousa da Silva, Alan and Altenhoff, Adrian and Huerta-Cepas, Jaime and Muffato, Matthieu and Patricio, Mateus and Vandepoele, Klaas and Ebersberger, Ingo and Blake, Judith and Fernandez Breis, Jesualdo Tomas and Boeckmann, Brigitte and Gabaldon, Toni and Sonnhammer, Erik and Dessimoz, Christophe and Lewis, Suzanna},
  issn         = {1367-4803},
  journal      = {BIOINFORMATICS},
  keyword      = {FUNCTIONAL ANNOTATIONS,SEQUENCE,TREE},
  language     = {eng},
  number       = {2},
  pages        = {323--329},
  title        = {Gearing up to handle the mosaic nature of life in the quest for orthologs},
  url          = {http://dx.doi.org/10.1093/bioinformatics/btx542},
  volume       = {34},
  year         = {2018},
}

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