skDER & CiDDER:微生物基因组复制的两个可扩展的方法
Rauf Salamzade1,2, Aamuktha Kottapalli1, Lindsay R Kalan1,3,4
1Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.
bioRxiv : the preprint server for biology
|December 4, 2023
概括
我们开发了skDER和CiDDER以实现高效的基因组复制,为比较基因组学选择代表性的微生物基因组. 这些工具有助于管理大型数据集,并减少进化分析中的偏见.
科学领域:
- 微生物基因组学 微生物基因组学
- 生物信息学是一种生物信息学.
- 进化生物学是进化的生物学.
背景情况:
- 越来越多的被测序微生物基因组对比性研究提出了计算挑战.
- 由于采样偏差,某些血统的过度代表性可能会扭曲进化分析.
研究的目的:
- 为基因组复制开发高效的工具,使得代表性基因组的选择可用于比较基因组研究.
- 解决与分析大规模微生物基因组数据集相关的计算负担和偏见.
主要方法:
- skDER:使用先进的算法快速平均核酸标识 (ANI) 估计和基因组复制.
- CiDDER:采用蛋白质聚类来代地选择代表性基因组,直到达到所需的蛋白质空间和.
- 辅助功能包括自动化基因组下载,非代表性的聚类和移动遗传元素 (MGE) 的过.
主要成果:
- skDER和CiDDER为选择代表性微生物基因组提供了高效的解决方案.
- 过MGE被发现稍微降低了一种物种基因组之间的ANI和对齐分数 (AF) 估计.
- 开发的工具提供了增强可用性和简化比较基因组工作流程的功能.
结论:
- skDER和CiDDER促进了更容易管理和更准确的比较基因组研究.
- 了解MGE对基因组指标的影响对于准确的下游分析至关重要.
- 这些工具有助于研究人员导航大型微生物基因组数据集以获得进化见解.
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