A model-based approach for detecting coevolving positions in a molecule
A model-based approach for detecting coevolving positions in a molecule
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DOI：
10.1093/molbev/msi183
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发表时间：
2005-09-01
影响因子：
10.7
通讯作者：
Galtier, N
中科院分区：
文献类型：
--
作者：
Dutheil, J;Pupko, T;Galtier, N
我们提出了一种检测分子中共同进化位点的新方法。该方法依赖于一组对齐的序列（核酸或蛋白质），并使用马尔可夫进化模型将发生在每个位点的替换映射到潜在的系统发育树的分支上。这种映射考虑了祖先状态和站点间速率变化的不确定性。然后，我们为每个位点构建一个“替代向量”，其中包含每个分支中替换数量的后验估计。然后将一对位点的共同进化量作为两个相应替代向量之间的Pearson相关系数进行测量，并与独立性零假设下的期望进行比较。我们将该方法应用于79种细菌核糖体RNA数据集，在过去的30年里，已经对这些数据集进行了广泛的结构表征。超过95%的分子内预测位点对与已知的相互作用位点对相对应。
We present a new method for detecting coevolving sites in molecules. The method relies on a set of aligned sequences (nucleic acid or protein) and uses Markov models of evolution to map the substitutions that occurred at each site onto the branches of the underlying phylogenetic tree. This mapping takes into account the uncertainty over ancestral states and among-site rate variation. We then build, for each site, a "substitution vector" containing the posterior estimates of the number of substitutions in each branch. The amount of coevolution for a pair of sites is then measured as the Pearson correlation coefficient between the two corresponding substitution vectors and compared to the expectation under the null hypothesis of independence. We applied the method to a 79-species bacterial ribosomal RNA data set, for which extensive structural characterization has been done over the last 30 years. More than 95% of the intramolecular predicted pairs of sites correspond to known interacting site pairs.