Comparison of methods for estimating the nucleotide substitution matrix.
Comparison of methods for estimating the nucleotide substitution matrix.
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DOI：
10.1186/1471-2105-9-511
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发表时间：
2008-12-01
影响因子：
3
通讯作者：
Knight R
中科院分区：
文献类型：
--
作者：
Oscamou M;McDonald D;Yap VB;Huttley GA;Lladser ME;Knight R
核苷酸取代率矩阵是分子进化的关键参数。已经提出了几种具有不同数学基础的推断该参数的方法。这些方法包括计算序列差异并取所得概率矩阵的对数、基于马尔可夫三元组的方法以及推断导致最可能的进化模型的替代概率的最大似然方法。然而，这些方法的速度和准确性尚未进行比较。不同方法的性能存在数量级差异（每个矩阵从 1 毫秒到 10 秒），但速率矩阵重建的精度差异似乎相对较小。令人鼓舞的是，相对简单和快速的方法可以提供至少与更复杂和计算密集的方法一样准确的结果，特别是当要比较的序列相对较短时。根据测试的条件，我们推荐使用 Gojobori 等人的方法。 (1982) 对于长序列（> 600 个核苷酸），以及 Goldman 等人的方法。 (1996) 对于较短的序列（< 600 个核苷酸）。 Barry 和 Hartigan (1987) 的方法可以在长序列（> 2000 个核苷酸）上提供更高的精度（以真实矩阵和推断矩阵之间的欧几里得距离来衡量），但代价是计算时间明显更长。快速而准确的方法的可用性将使我们能够获得生命树全基因组范围内核苷酸取代率矩阵变化的全局图景。
The nucleotide substitution rate matrix is a key parameter of molecular evolution. Several methods for inferring this parameter have been proposed, with different mathematical bases. These methods include counting sequence differences and taking the log of the resulting probability matrices, methods based on Markov triples, and maximum likelihood methods that infer the substitution probabilities that lead to the most likely model of evolution. However, the speed and accuracy of these methods has not been compared. Different methods differ in performance by orders of magnitude (ranging from 1 ms to 10 s per matrix), but differences in accuracy of rate matrix reconstruction appear to be relatively small. Encouragingly, relatively simple and fast methods can provide results at least as accurate as far more complex and computationally intensive methods, especially when the sequences to be compared are relatively short. Based on the conditions tested, we recommend the use of method of Gojobori et al. (1982) for long sequences (> 600 nucleotides), and the method of Goldman et al. (1996) for shorter sequences (< 600 nucleotides). The method of Barry and Hartigan (1987) can provide somewhat more accuracy, measured as the Euclidean distance between the true and inferred matrices, on long sequences (> 2000 nucleotides) at the expense of substantially longer computation time. The availability of methods that are both fast and accurate will allow us to gain a global picture of change in the nucleotide substitution rate matrix on a genomewide scale across the tree of life.
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影响因子：
3
作者：
Hamady M;Betterton MD;Knight R
通讯作者：
Knight R
影响因子：
12.3
作者：
Knight R;Maxwell P;Birmingham A;Carnes J;Caporaso JG;Easton BC;Eaton M;Hamady M;Lindsay H;Liu Z;Lozupone C;McDonald D;Robeson M;Sammut R;Smit S;Wakefield MJ;Widmann J;Wikman S;Wilson S;Ying H;Huttley GA
通讯作者：
Huttley GA
影响因子：
3.9
作者：
GOJOBORI, T;LI, WH;GRAUR, D
通讯作者：
GRAUR, D
影响因子：
6.5
作者：
Jayaswal, Vivek;Robinson, John;Jermiin, Lars
通讯作者：
Jermiin, Lars
影响因子：
10.7
作者：
Blouin, MS;Yowell, CA;Dame, JB
通讯作者：
Dame, JB