Dimmic M W, Mindell D P, Goldstein R A
Department of Biology, University of Michigan, Ann Arbor 48109-1055, USA.
Pac Symp Biocomput. 2000:18-29. doi: 10.1142/9789814447331_0003.
An adjustable fitness model for amino acid site substitutions is investigated. This model, a generalization of previously developed evolutionary models, has several distinguishing characteristics: it separately accounts for the processes of mutation and substitution, allows for heterogeneity among substitution rates and among evolutionary constraints, and does not make any prior assumptions about which sites or characteristics of proteins are important to molecular evolution. While the model has fewer adjustable parameters than the general reversible mtREV model, when optimized it outperforms mtREV in likelihood analysis on protein-coding mitochondrial genes. In addition, the optimized fitness parameters of the model show correspondence to some biophysical characteristics of amino acids.
研究了一种用于氨基酸位点替换的可调适应度模型。该模型是先前开发的进化模型的推广，具有几个显著特征：它分别考虑了突变和替换过程，允许替换率和进化约束之间存在异质性，并且不对蛋白质的哪些位点或特征对分子进化很重要做任何先验假设。虽然该模型的可调参数比一般的可逆mtREV模型少，但在对蛋白质编码线粒体基因的似然分析中进行优化后，它的表现优于mtREV。此外，该模型优化后的适应度参数显示出与氨基酸的一些生物物理特征相对应。
