Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, AZ 85719, United States; BIO5 Research Institute, University of Arizona, Tucson, AZ 85719, United States.
Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, AZ 85719, United States.
Virus Res. 2018 Jan 15;244:110-115. doi: 10.1016/j.virusres.2017.10.019. Epub 2017 Nov 1.
A plethora of tools exist for identifying phage sequences in bacterial genomes, single cell amplified genomes, and host-associated and environmental metagenomes. Yet because the genetics of phages and their hosts are closely intertwined, distinguishing viral from bacterial signal remains an ongoing challenge. Further the size, quantity and fragmentary nature of modern 'omics datasets ushers in a new set of computational challenges. Here, we detail the promises and pitfalls of using currently available gene-centric or k-mer based tools for identifying prophage sequences in genomes and prophage and viral contigs in metagenomes. Each of these methods offers a unique piece of the puzzle to elucidating the intriguing signatures of phage-host coevolution.
有大量的工具可用于识别细菌基因组、单细胞扩增基因组、宿主相关和环境宏基因组中的噬菌体序列。然而，由于噬菌体及其宿主的遗传学密切相关，因此区分病毒和细菌信号仍然是一个持续的挑战。此外，现代“组学”数据集的大小、数量和片段性质带来了一系列新的计算挑战。在这里，我们详细介绍了使用当前可用的基于基因或 k -mer 的工具来识别基因组中的原噬菌体序列以及宏基因组中的原噬菌体和病毒基因序列的优缺点。这些方法中的每一种都为阐明噬菌体-宿主共同进化的有趣特征提供了独特的拼图。
