A reliable sequence alignment method based on probabilities of residue correspondences
A reliable sequence alignment method based on probabilities of residue correspondences
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DOI：
10.1093/protein/8.10.999
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发表时间：
1995-10-01
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影响因子：
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通讯作者：
Miyazawa, S
中科院分区：
文献类型：
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作者：
Miyazawa, S
通过假设每个比对的统计权重与其总相似性得分的指数成正比来评估残基在比对中的所有可能对应的概率，基于这样的概率，提出了包括最可能对应的概率比对，在高度相似的序列对的情况下，概率比对与与具有最大相似性得分的比对相对应的最大相似性比对一致，概率比对中的显着对应是那些概率> 0.5的对应，将概率比对方法应用于一些蛋白质对，结果表明，概率比对中这种高度可能的对应可能是与结构比对一致的正确对应，而最大相似性比对中的错误对应通常是微不足道的。概率比对中的对应，概率比对中显着对应的对应残基叠加的均方根偏差往往比最大相似性比对中的所有对应更小，这表明最大相似性比对中的不正确对应往往是概率比对中的不显着对应，这一事实也在109个彼此相似、序列同一性在90%到35%之间的蛋白质对中得到证实，此外，概率比对方法可以更好地预测正确的与最大相似性对齐方法相比，概率对齐确实依赖于评分方案，但对诸如间隙惩罚之类的参数值不太敏感。本概率对齐方法对于基于对应概率构建可靠的对齐非常有用，并且可以与任何评分方案一起使用。
Probabilities of all possible correspondences of residues in aligning two proteins are evaluated by assuming that the statistical weight of each alignment is proportional to the exponent of its total similarity score, Based on such probabilities, a probability alignment that includes the most probable correspondences is proposed, In the cases of highly similar sequence pairs, the probability alignments agree with the maximum similarity alignments that correspond to the alignments with the maximum similarity score, Significant correspondences in the probability alignments are those whose probabilities are >0.5, The probability alignment method is applied to a few protein pairs, and results indicate that such highly probable correspondences in the probability alignments are probably correct correspondences that agree with the structural alignments and that incorrect correspondences in the maximum similarity alignments are usually insignificant. correspondences in the probability alignments, The root mean square deviations in superimposition of corresponding residues tend to be smaller for significant correspondences in the probability alignments than for all correspondences in the maximum similarity alignments, indicating that incorrect correspondences in the maximum similarity alignments tend to be insignificant correspondences in probability alignments, This fact is also confirmed in 109 protein pairs that are similar to each other with sequence identities between 90 and 35%, In addition, the probability alignment method may better predict correct correspondences than the maximum similarity alignment method, Probability alignments do, of course, depend on a scoring scheme but are less sensitive to the value of parameters such as gap penalties, The present probability alignment method is useful for constructing reliable alignments based on the probabilities of correspondences and can be used with any scoring scheme.