Computational approaches to predict bacteriophage-host relationships.
Computational approaches to predict bacteriophage-host relationships.
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DOI：
10.1093/femsre/fuv048
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发表时间：
2016-03
影响因子：
11.3
通讯作者：
Dutilh BE
中科院分区：
文献类型：
--
作者：
Edwards RA;McNair K;Faust K;Raes J;Dutilh BE
宏基因组学改变了病毒发现的面貌，它使病毒基因组序列的准确鉴定成为可能，而不需要分离病毒。因此，宏基因组病毒的发现留下了关于任何新病毒的第一个也是最基本的问题没有回答：病毒感染什么宿主？全球病毒圈的多样性和宏基因组测序项目中获得的大量数据需要用于病毒宿主预测的计算工具。我们专注于噬菌体（噬菌体，感染细菌的病毒），在环境宏基因组中发现的最丰富和最多样化的病毒组。通过分析820个带有注释的宿主，我们回顾并评估了计算机模拟噬菌体-宿主信号的预测能力。序列同源性方法在鉴定已知的噬菌体-宿主对方面是最有效的。基于组成和丰度的方法包含用于噬菌体-宿主分类的重要信号，为分析病毒宏基因组中的未知物提供了机会。总之，这些计算方法进一步加深了我们对细菌与宿主之间相互作用的了解。重要的是，我们发现，所有审查的信号显着链接到他们的主机，说明如何利用目前的知识和见解的相互作用机制和生态学的共同进化的细菌和细菌可以预测噬菌体-宿主关系，与潜在的相关性的医疗和工业应用。通过基于序列的探索，在许多环境中越来越多地发现感染细菌的新病毒。为了了解它们在微生物生态系统中的作用，计算工具对于优先考虑和指导实验工作是必不可少的。这篇综述评估和讨论了一系列生物信息学方法来预测噬菌体-宿主关系时，所有已知的是他们的基因组序列。
Metagenomics has changed the face of virus discovery by enabling the accurate identification of viral genome sequences without requiring isolation of the viruses. As a result, metagenomic virus discovery leaves the first and most fundamental question about any novel virus unanswered: What host does the virus infect? The diversity of the global virosphere and the volumes of data obtained in metagenomic sequencing projects demand computational tools for virus–host prediction. We focus on bacteriophages (phages, viruses that infect bacteria), the most abundant and diverse group of viruses found in environmental metagenomes. By analyzing 820 phages with annotated hosts, we review and assess the predictive power of in silico phage–host signals. Sequence homology approaches are the most effective at identifying known phage–host pairs. Compositional and abundance-based methods contain significant signal for phage–host classification, providing opportunities for analyzing the unknowns in viral metagenomes. Together, these computational approaches further our knowledge of the interactions between phages and their hosts. Importantly, we find that all reviewed signals significantly link phages to their hosts, illustrating how current knowledge and insights about the interaction mechanisms and ecology of coevolving phages and bacteria can be exploited to predict phage–host relationships, with potential relevance for medical and industrial applications. New viruses infecting bacteria are increasingly being discovered in many environments through sequence-based explorations. To understand their role in microbial ecosystems, computational tools are indispensable to prioritize and guide experimental efforts. This review assesses and discusses a range of bioinformatic approaches to predict bacteriophage–host relationships when all that is known is their genome sequence.
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影响因子：
4.4
作者：
Beumer, A;Robinson, JB
通讯作者：
Robinson, JB
影响因子：
5.2
作者：
Aziz RK;Dwivedi B;Akhter S;Breitbart M;Edwards RA
通讯作者：
Edwards RA
影响因子：
4.2
作者：
Anderson, Rika E.;Brazelton, William J.;Baross, John A.
通讯作者：
Baross, John A.
DOI：
10.1534/g3.114.011825
发表时间：
2014-05-22
期刊：
G3 (Bethesda, Md.)
影响因子：
--
作者：
Burton JN;Liachko I;Dunham MJ;Shendure J
通讯作者：
Shendure J
影响因子：
4.1
作者：
Biswas A;Gagnon JN;Brouns SJ;Fineran PC;Brown CM
通讯作者：
Brown CM