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埃芬德 (EEfinder) 是一种通用工具,用于识别真核基因组中的细菌和病毒内源化元素

Yago José Mariz Dias^1,2,3, Filipe Zimmer Dezordi^1,2, Gabriel da Luz Wallau^1,2,4,5

¹Núcleo de Bioinformática, Instituto Aggeu Magalhães (IAM), Fundação Oswaldo Cruz (FIOCRUZ), Recife, PE, Brazil.

Computational and structural biotechnology journal

|November 5, 2024

概括

一个新的工具,EEfinder,系统地识别和分类结合到真核生物基因组中的病毒和细菌遗传物质. 这有助于理解宿主-病原体进化,并提高了元基因组研究的准确性.

科学领域:

基因组学就是基因组学.
分子生物学分子生物学
生物信息学是一种生物信息学.

背景情况:

横向基因转移 (HGT) 便于在没有直接血统的物种之间进行遗传物质交换.
在真核基因组中的内源性病毒元素 (EVE) 和细菌元素提供了对过去宿主-病原体相互作用和共同进化的洞察.
现有的识别这些元素的方法缺乏标准化,阻碍了可重复性和比较分析.

研究的目的:

推出EEfinder,这是一种多功能,标准化的工具,用于识别和分类真核生物基因组中的病毒和细菌内源元素.
提供一种可复制和系统的方法来分析来自真核DNA中的病毒和细菌的遗传物质.

主要方法:

EEfinder整合了六个关键步骤:数据清理,序列对齐以进行相似性搜索,候选元素过,分类学赋值,合并截断的元素和侧面提取.
该工具通过将其性能与已发表的文献数据和湿实验室实验结果进行比较来评估.

主要成果:

与手动策划的数据相比,EEfinder成功识别了97%的内源性病毒元素 (EVE).
该工具准确地检测到Wolbachia基因组的几乎完整整合,并通过实验结果验证了其有效性.

结论:

EEfinder提供了一种有效和系统的解决方案,用于识别和分类真核生物基因组中的细菌和病毒内源元素.
该工具提高了基因组分析的可靠性,支持进化研究,并促进了准确的元基因组数据解释.

关键词:

细菌细菌是一种细菌.进行比较的基因组学.基因组的演变基因组的演变整合整合整合同生动物是共生动物.病毒病毒病毒

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