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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update.Galaxy 平台,用于实现可访问、可重现和协作的生物医学分析:2020 年更新。
Nucleic Acids Res. 2020 Jul 2;48(W1):W395-W402. doi: 10.1093/nar/gkaa434.
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tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences.tRNAscan-SE:在基因组序列中搜索tRNA基因。
Methods Mol Biol. 2019;1962:1-14. doi: 10.1007/978-1-4939-9173-0_1.
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Apollo: Democratizing genome annotation.阿波罗:基因组注释的民主化。
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Parallel Evolution of Host-Attachment Proteins in Phage PP01 Populations Adapting to O157:H7.噬菌体PP01群体中宿主附着蛋白在适应O157:H7过程中的平行进化
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PeerJ. 2013 Sep 17;1:e167. doi: 10.7717/peerj.167. eCollection 2013.
8
Structure of the receptor-binding carboxy-terminal domain of bacteriophage T7 tail fibers.噬菌体 T7 尾丝受体结合羧基末端结构域。
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9
SignalP 4.0: discriminating signal peptides from transmembrane regions.信号肽预测工具SignalP 4.0:区分信号肽与跨膜区域。
Nat Methods. 2011 Sep 29;8(10):785-6. doi: 10.1038/nmeth.1701.
10
The gp38 adhesins of the T4 superfamily: a complex modular determinant of the phage's host specificity.T4 超家族的 gp38 黏附素:噬菌体宿主特异性的复杂模块决定因素。
Genome Biol Evol. 2011;3:674-86. doi: 10.1093/gbe/evr059. Epub 2011 Jul 11.

噬菌体Ac3针对ECOR参考文库的基因组注释及宿主范围分析。

Phage Ac3's Genome Annotation and Host Range Analysis Against the ECOR Reference Library.

作者信息

Farquharson Emma L, Nugen Sam R

机构信息

Department of Food Science, Cornell University, Ithaca, New York, USA.

出版信息

Phage (New Rochelle). 2022 Sep 1;3(3):165-170. doi: 10.1089/phage.2022.0008. Epub 2022 Sep 19.

DOI:10.1089/phage.2022.0008
PMID:36199530
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9527048/
Abstract

Host range analyses and genome sequencing/annotation of bacteriophage isolates allow more effective development of tools for applications in medicine, agriculture, and the environment and expand our understanding of phage biology. Here we present the complete sequence of phage Ac3's assembled and annotated genome (accession OK040907). Originally referred to simply as "3," Ac3 has previously been described as a T4-like bacteriophage belonging to the family in the order of tailed bacteriophages. Using a combination of spot tests and full plate plaque assays, Ac3's permissive and adsorptive host range were evaluated against the ECOR Reference Library; a panel of 72 isolates meant to represent the diversity of . Spot assays revealed that Ac3 could adsorb to 43 of the 72 strains (59.7%), whereas plaque assays demonstrated Ac3's ability to complete replication within 27 of the 72 strains (37.5%). By overlaying spot test and plaque assay results, 16 of the 45 nonpermissive ECOR strains (35.5%) were highlighted as being able to support Ac3's adsorption and tail contraction, but not its replication. Further characterization of Ac3 is still needed, however, the study presented here provides a solid starting point for future research.

摘要

噬菌体分离株的宿主范围分析以及基因组测序/注释,有助于更有效地开发用于医学、农业和环境应用的工具,并扩展我们对噬菌体生物学的理解。在此,我们展示了噬菌体Ac3组装和注释后的基因组完整序列(登录号OK040907)。Ac3最初简称为“3”,此前被描述为一种属于有尾噬菌体目家族的T4样噬菌体。使用点滴试验和全平板噬菌斑测定相结合的方法,针对ECOR参考文库评估了Ac3的允许宿主范围和吸附宿主范围;该文库由72株分离株组成,旨在代表的多样性。点滴试验表明,Ac3可以吸附72株菌株中的43株(59.7%),而噬菌斑测定表明Ac3能够在72株菌株中的27株(37.5%)内完成复制。通过叠加点滴试验和噬菌斑测定结果,45株非允许ECOR菌株中的16株(35.5%)被突出显示为能够支持Ac3的吸附和尾部收缩,但不能支持其复制。然而,仍需要对Ac3进行进一步表征,本文提出的研究为未来的研究提供了一个坚实的起点。