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HMMPolish:用于TGS测序RNA病毒的编码区域抛光工具

Runzhou Yu¹, Syed Muhammad Umer Abdullah¹, Yanni Sun¹

¹Electrical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China.

Briefings in bioinformatics

|July 21, 2023

概括

一个新的工具HMMPolish通过纠正蛋白质编码区域的错误来提高病毒基因组的准确性. 该管道增强了第三代测序 (TGS) 数据,以实现更可靠的病毒分析和血统识别.

科学领域:

基因组学就是基因组学.
生物信息学是一种生物信息学.
病毒学病毒学

背景情况:

准确的病毒基因组对于下游分析至关重要,例如血统识别和变种监测.
第三代测序 (TGS) 为病毒测序提供了长读数,但其错误率高于下一代测序.
现有的抛光工具看起来很有前途,但在纠正错误方面存在局限性,特别是在编码区域内.

研究的目的:

开发一种新的管道,HMMPolish,用于纠正已知RNA病毒的蛋白质编码区域中的错误.
为了提高从TGS数据的病毒基因组组装的准确性.
解决当前抛光工具在关键基因组区域内处理错误方面的局限性.

主要方法:

开发了HMMPolish,这是一个利用蛋白质家族/域的隐藏马尔科夫模型 (HMM) 配置文件的管道.
应用HMMPolish到原始TGS读数和组装序列.
使用HMM来识别和纠正其他抛光器错过的错误,专注于蛋白质编码区域.

主要成果:

在RNA病毒的蛋白质编码区域中,HMMPolish证明了有效的错误校正.
在34个数据集上验证,涵盖HIV-1,流感-A,诺罗病毒和SARS-CoV-2.
在基准测试中表现优于或有利于与流行的抛光工具竞争.

结论:

HMMPolish为纠正病毒蛋白编码区域的错误提供了显著的改进.
该工具提高了从TGS数据的病毒基因组组装的准确性.
在RNA病毒中,HMMPolish对于准确的血统识别和变异监测非常有价值.

关键词:

核糖核酸 (RNA) 病毒第三代测序 (TGS) 系统对于TGS组件的抛光机.简介 HMMs 的 HMMs.

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