Helmholtz Gemeinschaft

Search
Browse
Statistics
Feeds

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

[thumbnail of 17343oa.pdf]
Preview
PDF - Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader
364kB

Item Type:Article
Title:Gearing up to handle the mosaic nature of life in the quest for orthologs
Creators Name: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, J.T., Boeckmann, B., Gabaldón, T., Sonnhammer, E., Dessimoz, C. and Lewis, S.
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.
Source:Bioinformatics
ISSN:1367-4803
Publisher:Oxford University Press
Volume:34
Number:2
Page Range:323-329
Date:15 January 2018
Official Publication:https://doi.org/10.1093/bioinformatics/btx542
PubMed:View item in PubMed

Repository Staff Only: item control page

Downloads

Downloads per month over past year

Open Access
MDC Library