Modeling residue usage in aligned protein sequences via maximum likelihood
Modeling residue usage in aligned protein sequences via maximum likelihood
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DOI：
10.1093/oxfordjournals.molbev.a025583
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发表时间：
1996-12-01
影响因子：
10.7
通讯作者：
Bruno, WJ
中科院分区：
文献类型：
--
作者：
Bruno, WJ
提出了一种计算方法来表征比对蛋白质序列中残基的使用，即特定位置的残基频率。该方法在给定由其他方法计算的一棵树或一组候选树的情况下，获得在用于序列进化的简单模型中最大化序列的似然的频率估计。这些最大似然频率构成了序列的轮廓，因此该方法提供了用于构建这种轮廓的序列加权的严格替代。这种方法能够消除误导性的系统发育效应，从而可以更清楚地观察和解释序列中不同位置的生化倾向。
A computational method is presented for characterizing residue usage, i.e., site-specific residue frequencies, in aligned protein sequences. The method obtains frequency estimates that maximize the likelihood of the sequences in a simple model for sequence evolution, given a tree or a set of candidate trees computed by other methods. These maximum-likelihood frequencies constitute a profile of the sequences, and thus the method offers a rigorous alternative to sequence weighting for constructing such a profile. The ability of this method to discard misleading phylogenetic effects allows the biochemical propensities of different positions in a sequence to be more clearly observed and interpreted.