Syn-CpG-Spacer:一个面板网络应用程序,用于用CpG二核酸重新编码病毒基因组
Aleksander Sulkowski1, Clément Bouton1, Chad Swanson1
1Department of Infectious Diseases, King's College London, London, United Kingdom.
Journal of open source software
|April 23, 2024
概括
脊椎动物病毒通常具有较低的CpG频率,以逃避宿主防御. Syn-CpG-Spacer是一种工具,允许研究人员在病毒序列中增加CpG二核酸,帮助病毒衰减,同时保持抗原性.
科学领域:
- 病毒学和生物信息学
- 基因组序列分析和操纵
背景情况:
- 脊椎动物的基因组表现出CpG二核酸的自然枯竭.
- 许多脊椎动物病毒已经进化到模仿这种低CpG成分,以逃避宿主抗病毒防御,例如ZAP蛋白.
- 病毒基因组中的CpG枯竭也可能是其他选择性压力的结果.
研究的目的:
- 通过同义重编码开发一种工具来增加病毒序列中的CpG二核酸丰富度.
- 通过修改非CpG编码子来促进病毒衰减而不会损害表皮质抗原性.
- 为分析和操纵病毒性CpG内容提供一个用户友好的平台.
主要方法:
- 开发 Syn-CpG-Spacer,这是一个使用 Panel 库的 Python 渐进式 Web 应用程序 (PWA).
- 实施CpG重新编码的生物相关约束,包括最小间隙,平均间隙优化,监管信号保护和A内容调制.
- 整合了 Biopython 模块用于 FASTA 文件输入/输出,以及基于 Bokeh 的序列查看器用于 CpG 可视化,完全通过 Pyodide 在用户浏览器中运行.
主要成果:
- Syn-CpG-Spacer应用程序使病毒序列的连续重新编码能够增加CpG二核酸的频率.
- 用户可以应用特定的约束来指导重新编码过程,确保生物相关性.
- 交互式序列查看器和统计表可方便对记录后的CpG分布进行有效分析.
结论:
- 同义重编码提供了一个可行的策略,通过增加CpG丰富度来减弱病毒.
- Syn-CpG-Spacer为研究人员提供了一种强大且易于使用的工具,以探索病毒基因组中的CpG操纵.
- PWA的基于浏览器的执行和离线功能增强了它对科学界的实用性.
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