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首页> 外文期刊>Journal of Molecular Biology >AN ASSESSMENT OF AMINO ACID EXCHANGE MATRICES IN ALIGNING PROTEIN SEQUENCES - THE TWILIGHT ZONE REVISITED
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AN ASSESSMENT OF AMINO ACID EXCHANGE MATRICES IN ALIGNING PROTEIN SEQUENCES - THE TWILIGHT ZONE REVISITED

机译：氨基酸序列交换中氨基酸交换矩阵的评估-暮光区

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摘要

The sensitivity of most protein sequence alignment methods depends strongly on the quality of the comparison matrices used. These matrices, which assign weights or similarity scores to every possible amino acid substitution pair, are utilized to differentiate amongst the various possible alignments of two or more sequences. There are many ways to generate these exchange weights and new matrices are constantly published. There has been no overall assessment of these various matrices when applied in different alignment techniques and over many protein folds and families, both close and distant and with the use of several gap penalty values. In this work, a set of amino acid sequences matched by superposition of known protein tertiary topologies is used to test the alignment accuracy of the different method/matrix/penalty combinations. The comparisons show relatively similar results for the top scoring matrices, a preference for the global alignment method of Needleman and Wunsch, and the importance of matrix modification and optimized gap penalties. The relationship between the percentage identity in a resulting alignment and the level of correctness to be expected are given for the top-performing matrix, resulting in a better definition of the so-called ''twilight zone''. Estimates are made for the probability that two sequences, aligned at a certain level of residue percentage identity, are in fact unrelated. [References: 41]
机译：大多数蛋白质序列比对方法的灵敏度在很大程度上取决于所用比较基质的质量。这些矩阵为每个可能的氨基酸取代对分配权重或相似性分数，用于区分两个或多个序列的各种可能的比对。有很多方法可以产生这些交换权重，并且不断发布新的矩阵。当将这些矩阵应用于不同的比对技术时，对于许多蛋白质折叠和家族，无论是近距离还是远距离，以及使用多个空位罚分值，都没有整体评估。在这项工作中，一组氨基酸序列与已知蛋白质三级拓扑结构的叠加相匹配，用于测试不同方法/矩阵/罚分组合的比对准确性。比较结果显示得分最高的矩阵相对相似，偏爱Needleman和Wunsch的全局比对方法，矩阵修改和优化缺口罚分的重要性。对于性能最高的矩阵，给出了结果对齐中的百分比同一性和预期的正确性之间的关系，从而更好地定义了所谓的“暮光区”。对在一定水平的残基百分比同一性上比对的两个序列实际上不相关的概率进行估计。 [参考：41]

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