Gearing up to handle the mosaic nature of life in the quest for orthologs
Gearing up to handle the mosaic nature of life in the quest for orthologs
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DOI：
10.1093/bioinformatics/btx542
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发表时间：
2018-01-15
期刊：
影响因子：
5.8
通讯作者：
Lewis, Suzanna
中科院分区：
文献类型：
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作者：
Forslund, Kristoffer;Pereira, Cecile;Lewis, Suzanna
Quest for Orthologs (QfO) 是一个开放式协作框架，为比较系统发育组学和相关研究领域对高精度直系预测及其应用感兴趣的专家提供。我们在此报告 2015 年在巴塞罗那举行的 QfO 会议的要点和讨论要点。近年来的成就为支持改进同源预测和探索新方法的发展奠定了基础。 QfO 工作的核心是方法和服务的适当基准测试，以及标准化数据集和标准化格式的设计，以允许结果共享和比较。同时，分析管道得到了改进、评估和调整，以处理大型数据集。如果没有联盟成员的长期合作，这一切都不会发生。定期召开会议来审查和协调广泛的创新研究人员的补充活动显然有利于社区。会议的重点包括解决直系同源调用之间分歧的来源和合法性、直系同源定义的上下文依赖性、在分析非常古老的直系同源时遇到的特殊挑战、全基因组重复的直系同源，以及不同级别的直系同源与旁系同源关系的概念，包括域级直系同源。此外，还讨论了不同应用（例如植物基因组学、古代基因家族等）的特殊需求以及用于进行直系同源推理的基础设施（例如与模式生物数据库的接口），以及预计将在即将召开的 2017 年 QfO 会议期间报告的几项正在进行的工作。
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.