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在模拟的古老和现代的元基因组数据上对元基因组分类器进行基准测试
Vaidehi Pusadkar1,2, Rajeev K Azad1,2,3
1Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA.
Microorganisms
|October 28, 2023
概括
评估古老的元基因组概况是非常重要的. 人类和环境污染显著影响性能,超过DNA损伤. DNA-to-DNA和DNA-to-marker方法为改善古代微生物组分析提供了互补的优势.
科学领域:
- 古代的DNA研究研究.
- 微生物组的分析
- 生物信息学是一种生物信息学.
背景情况:
- 古代元基因组样本分析受到DNA降解的阻碍.
- 现有的元基因组分析仪主要在现代或模拟的现代样本上进行测试.
- 缺少在整个降解频谱中对分析器性能进行全面的比较.
研究的目的:
- 在模拟的古代DNA上评估各种元基因组造型器的性能.
- 评估不同DNA损伤模式 (除菌,碎片,污染) 对分析器准确性的影响.
- 确定古代元基因组的不同分析方法的优点和弱点.
主要方法:
- 人类牙结石微生物组的模拟元基因组被创建,DNA损伤水平不断增加.
- 评估了三个类型的造型剂 (DNA-to-DNA,DNA-to-蛋白质,DNA-to-标记物).
- 模拟的除毒,碎片化和污染被应用到模仿古老的DNA特征.
主要成果:
- 与排毒和碎片化相比,人类和环境污染对形仪性能产生了最显著的负面影响.
- DNA-to-DNA分析仪 (例如,Kraken2,Bracken) 和DNA-to-marker分析仪 (例如,MetaPhlAn4) 显示出不同的性能特征.
- 分析者的有效性因模拟的DNA损伤的类型和程度而异.
结论:
- 古代DNA污染是影响元基因组分析准确性的关键因素.
- 将DNA与DNA和DNA与标记者的方法结合起来,可以提高古代微生物组分析的可靠性.
- 为了进行强大的古代元基因组分析,需要进一步开发和验证配置文件.
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