Efficient methods for estimating amino acid replacement rates
Efficient methods for estimating amino acid replacement rates
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DOI：
10.1007/s00239-004-0113-9
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发表时间：
2006-06-01
影响因子：
3.9
通讯作者：
Arvestad, Lars
中科院分区：
文献类型：
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作者：
Arvestad, Lars
替换率矩阵描述了蛋白质中某一位置的进化过程，并用于从进化角度研究蛋白质的许多应用中。已经提出了几个通用矩阵，并且已被证明是真实过程的良好近似。然而，有些数据不适合使用通用矩阵，例如特殊的蛋白质家族、生命树中的某些谱系或蛋白质的特定部分。对此类数据的分析可以受益于数据特定速率矩阵的调整。本文提出了两种根据独立的成对蛋白质序列比对估计替换率矩阵的新方法，并仔细研究了 Muller-Vingron 的解析方法。对合成数据集的综合测试表明，两种新方法在各种设置中都比解析方法表现得更好。此外，最佳方法还被证明在小型数据集上具有鲁棒性，并且在非常大的真实数据集上也很实用。不必丢弃短序列对或发散序列对，从而使该方法在数据方面非常经济。建议对多重比对数据进行泛化，并将其用于蛋白质结构域家族系统发育的测试，其中表明该方法提供了家族特异性速率矩阵，该矩阵通常比一般矩阵具有明显更好的可能性。
Replacement rate matrices describe the process of evolution at one position in a protein and are used in many applications where proteins are studied with an evolutionary perspective. Several general matrices have been suggested and have proved to be good approximations of the real process. However, there are data for which general matrices are inappropriate, for example, special protein families, certain lineages in the tree of life, or particular parts of proteins. Analysis of such data could benefit from adaption of a data-specific rate matrix. This paper suggests two new methods for estimating replacement rate matrices from independent pairwise protein sequence alignments and also carefully studies Muller-Vingron's resolvent method. Comprehensive tests on synthetic datasets show that both new methods perform better than the resolvent method in a variety of settings. The best method is furthermore demonstrated to be robust on small datasets as well as practical on very large datasets of real data. Neither short nor divergent sequence pairs have to be discarded, making the method economical with data. A generalization to multialignment data is suggested and used in a test on protein-domain family phylogenies, where it is shown that the method offers family-specific rate matrices that often have a significantly better likelihood than a general matrix.