Probabilistic reconstruction of ancestral protein sequences
Probabilistic reconstruction of ancestral protein sequences
复制标题
DOI：
10.1007/bf02198858
复制
发表时间：
1996-02-01
影响因子：
3.9
通讯作者：
Goldstein, RA
中科院分区：
文献类型：
--
作者：
Koshi, JM;Goldstein, RA
使用最大似然形式主义，我们已经开发出一种方法，重建祖先蛋白质的序列。我们的方法不仅可以计算最可能的祖先序列，而且可以计算进化树中任何给定节点上任何氨基酸的概率。因为我们在氨基酸水平上考虑进化，我们能够更好地包括进化压力的影响，并通过使用依赖于二级结构和表面可及性的突变矩阵来利用蛋白质的结构信息。该方法的计算复杂度与用于重建祖先序列的同源蛋白质的数量线性相关。
Using a maximum-likelihood formalism, we have developed a method with which to reconstruct the sequences of ancestral proteins. Our approach allows the calculation of not only the most probable ancestral sequence but also of the probability of any amino acid at any given node in the evolutionary tree. Because we consider evolution on the amino acid level, we are better able to include effects of evolutionary pressure and take advantage of structural information about the protein through the use of mutation matrices that depend on secondary structure and surface accessibility. The computational complexity of this method scales Linearly with the number of homologous proteins used to reconstruct the ancestral sequence.