DeepPL:一种基于深度学习的工具,用于预测菌体生命周期
Yujie Zhang1, Mark Mao2, Robert Zhang2
1Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California, United States of America.
PLoS computational biology
|October 17, 2024
概括
使用自然语言处理的新工具DeepPL,可以从核酸序列准确预测细菌菌体 (菌体) 的生命周期. 这种方法为菌体研究和转基因组学提供了传统实验的可靠替代方案.
科学领域:
- 病毒学 病毒学
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
背景情况:
- 菌体 (菌体) 呈现出不同的生命周期:溶性 (宿主溶解) 和溶性 (基因组整合).
- 准确的菌体生命周期识别对于开发基于菌体的应用至关重要.
- 确定菌体生命周期的传统生物实验是复杂和耗时的.
研究的目的:
- 开发和评估DeepPL,这是一个基于自然语言处理 (NLP) 的新工具,用于预测菌体生命周期.
- 用核酸序列评估DeepPL的性能,并将其与现有的预测算法进行比较.
- 探索DeepPL在病毒转基因组研究中的实用性.
主要方法:
- 开发DeepPL,一种基于NLP的工具,利用核酸序列用于菌体生命周期预测.
- 使用已建立的数据集进行性能评估,包括分离和验证的菌体.
- 在通过下一代测序生成的模拟菌体社区元基因组数据集上测试DeepPL.
主要成果:
- 在一般生命周期预测中,DeepPL实现了高精度 (94.65%),灵敏度 (92.24%) 和特异性 (95.91%).
- 对于先前分离和生物验证的菌体,DeepPL证明了100%的准确性.
- 在元基因组分析中,DeepPL在完整的菌体基因组上显示了100%的准确性,在菌体结合物上显示了71.14%-100%的准确性.
结论:
- DeepPL提供了一种可靠和准确的方法,直接从核酸序列预测菌体生命周期.
- 该工具的高性能表明其适用于基本菌体研究和复杂的元基因组学研究.
- 对于菌体生命周期的确定,DeepPL比传统的实验方法有了显著的进步.
相关概念视频
Lytic Cycle of Bacteriophages
70.4K
Bacteriophages, also known as phages, are specialized viruses that infect bacteria. A key characteristic of phages is their distinctive “head-tail” morphology. A phage begins the infection process (i.e., lytic cycle) by attaching to the outside of a bacterial cell. Attachment is accomplished via proteins in the phage tail that bind to specific receptor proteins on the outer surface of the bacterium. The tail injects the phage’s DNA genome into the bacterial cytoplasm. In the...
70.4K
Lysogenic Cycle of Bacteriophages
61.9K
In contrast to the lytic cycle, phages infecting bacteria via the lysogenic cycle do not immediately kill their host cell. Instead, they combine their genome with the host genome, allowing the bacteria to replicate the phage DNA along with the bacterial genome. The incorporated copy of the phage genome is called the prophage. Some prophages can re-activate and enter the lytic cycle. This often occurs in response to a perturbation, such as DNA damage, but can also transpire in the absence of...
61.9K
Viral Replication: Lysogenic Cycle
1
The lysogenic cycle is a crucial viral replication strategy that allows bacteriophages to persist within host cells without immediately destroying them. This process is primarily observed in temperate phages, such as bacteriophage lambda (λ), which infects Escherichia coli. The cycle allows the viral genome to persist across bacterial generations while keeping host cells viable.Integration of the Viral GenomeUpon infection, bacteriophage lambda attaches to the bacterial surface and injects...
1
Viral Replication: Lytic Cycle
7
Bacteriophages, or phages, are viruses that specifically infect bacteria. Among them, T-even bacteriophages, such as T4, exhibit a well-characterized lytic replication cycle in Escherichia coli (E. coli). This process ensures the rapid proliferation of the virus while ultimately leading to the destruction of the bacterial host.Attachment and DNA InjectionThe infection process begins with the recognition and binding of the T4 phage to the E. coli cell surface. Tail fibers of the phage...
7
CRISPR and crRNAs
16.9K
Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
The CRISPR-Cas system stores a copy of foreign DNA in the host genome and uses it to identify the foreign DNA upon reinfection. CRISPR-Cas has three different...
The CRISPR-Cas system stores a copy of foreign DNA in the host genome and uses it to identify the foreign DNA upon reinfection. CRISPR-Cas has three different...
16.9K


