MODELING AMINO ACID SUBSTITUTIONS FOR WHOLE GENOMES

L. Vinh
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引用次数: 1

Abstract

Modeling amino acid substitution process is a core task in bioinformatics. New advanced sequencing technologies have generated huge datasets including whole genomes from various species. Estimating amino acid substitution models from whole genome datasets provides us unprecedented opportunities to accurately investigate relationships among species. In this paper, we review state-of-the-art computational methods to estimate amino acid substitution models from large datasets. We also describe a comprehensive pipeline to practically estimate amino acid models from whole genome datasets. Finally, we apply amino acid substitution models to build phylogenomic trees from bird and plant genome datasets. We compare our newly reconstructed phylogenomic trees and published ones and discuss new findings.
模拟全基因组的氨基酸取代
氨基酸取代过程建模是生物信息学的核心问题。新的先进测序技术产生了庞大的数据集,包括来自不同物种的全基因组。从全基因组数据集估计氨基酸替代模型为我们提供了前所未有的机会来准确地研究物种之间的关系。在本文中,我们回顾了最先进的计算方法,以估计氨基酸取代模型从大数据集。我们还描述了一个全面的管道,以实际估计氨基酸模型从全基因组数据集。最后,我们应用氨基酸替代模型从鸟类和植物基因组数据集构建系统基因组树。我们比较了新重建的系统基因组树和已发表的系统基因组树,并讨论了新的发现。
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