Modeling amino acid replacement
Modeling amino acid replacement
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DOI：
10.1089/10665270050514918
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发表时间：
2000-01-01
影响因子：
1.7
通讯作者：
Vingron, M
中科院分区：
文献类型：
--
作者：
Müller, T;Vingron, M
分子进化过程中氨基酸替换频率的估计对于序列分析中的许多应用至关重要，数据库搜索程序或系统发育分析的评分矩阵依赖于这种蛋白质进化模型。 Dayhoff 等人 (1978) 做出了开创性的工作，他们制定了马尔可夫进化模型并导出了著名的 PAM 得分矩阵。她对氨基酸交换频率的估计程序仅限于具有恒定且较小程度分歧的蛋白质对。在这里，我们提出了一种改进的估计器，称为解析方法，它不受这些限制。 Dayhoff 方法的这种扩展使我们能够根据不同程度分歧的比对来估计氨基酸替代模型。广泛的模拟表明新的估计器能够准确恢复氨基酸之间的交换频率。基于对齐蛋白质家族的 SYSTERS 数据库（Krause 和 Vingron，1998），我们重新计算一系列评分矩阵。
The estimation of amino acid replacement frequencies during molecular evolution is crucial for many applications in sequence analysis, Score matrices for database search programs or phylogenetic analysis rely on such models of protein evolution. Pioneering work was done by Dayhoff et al, (1978) who formulated a Markov model of evolution and derived the famous PAM score matrices. Her estimation procedure for amino acid exchange frequencies is restricted to pairs of proteins that have a constant and small degree of divergence. Here we present an improved estimator, called the resolvent method, that is not subject to these limitations. This extension of Dayhoff's approach enables us to estimate an amino acid substitution model from alignments of varying degree of divergence. Extensive simulations show the capability of the new estimator to recover accurately the exchange frequencies among amino acids. Based on the SYSTERS database of aligned protein families (Krause and Vingron, 1998) we recompute a series of score matrices.