泛PA:泛蛋白质组图的生成和对齐
Fawaz Dabbaghie1,2,3, Sanjay K Srikakulam3,4,5, Tobias Marschall1,2
1Institute for Medical Biometry and Bioinformatics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.
Bioinformatics advances
|December 25, 2023
概括
亲核生物基因组多样性挑战了基于DNA的比较. 泛PA利用泛蛋白质组,对准氨基酸序列进行更全面的分析,显著提高了比较基因组学中的读取对准率.
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.
- 进行比较的基因组学.
背景情况:
- 益生菌基因组由于突变和水平基因转移而表现出高度多样性,导致线性基因组比较中的参考偏差.
- 由于这种多样性,DNA序列比较在 prokaryotes 中具有挑战性,尽管编码区域构成了基因组的大多数.
研究的目的:
- 为解决由高多样性引起的 prokaryotic 基因组比较的挑战.
- 为了利用更高的进化约束和氨基酸序列的相似性,进行更强大的基因组分析.
- 引入PanPA,一种基于图形的泛蛋白质组分析的新方法.
主要方法:
- PanPA对蛋白质序列进行多次序列对齐,并构建索引图.
- 该方法将DNA或氨基酸序列与这些图表对齐.
- 通过使用来自*大肠杆菌*和*大肠菌*组合的泛蛋白组来评估PanPA.
主要成果:
- 潘帕在大肠杆菌 (E. coli) 泛蛋白质组上显示了正确的对齐.
- 对*S. enterica*组件的比较显示,PanPA对*E. coli*参考进行了比传统方法更多的~22%的序列对齐.
- 对于全基因组测序数据,PanPA将68%的读数与BWA与*大肠杆菌*参考相匹配,而BWA为5%.
结论:
- 泛蛋白质组为各种 prokaryotic 基因组提供了基于 DNA 的比较的有效替代方案.
- 潘帕增强了序列对齐的准确性和覆盖范围,特别是在全基因组测序数据方面.
- 通过使用保存的蛋白质序列,PanPA方法改善了比较基因组学.
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