serval:BIB_D31584E0556C
Gearing up to handle the mosaic nature of life in the quest for orthologs.
10.1093/bioinformatics/btx542
000419593000027
28968857
Forslund
K.
author
Pereira
C.
author
Capella-Gutierrez
S.
author
Sousa da Silva
A.
author
Altenhoff
A.
author
Huerta-Cepas
J.
author
Muffato
M.
author
Patricio
M.
author
Vandepoele
K.
author
Ebersberger
I.
author
Blake
J.
author
Fernández Breis
J.T.
author
Quest for Orthologs Consortium
contributor
Boeckmann
B.
author
Gabaldón
T.
author
Sonnhammer
E.
author
Dessimoz
C.
co-last author
Lewis
S.
author
article
2018
Bioinformatics
1367-4811
1367-4803
journal
34
2
323-329
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.
eng
60_published
true
peer-reviewed
University of Lausanne
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