A STRUCTURAL BASIS FOR SEQUENCE COMPARISONS - AN EVALUATION OF SCORING METHODOLOGIES
A STRUCTURAL BASIS FOR SEQUENCE COMPARISONS - AN EVALUATION OF SCORING METHODOLOGIES
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DOI：
10.1006/jmbi.1993.1548
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发表时间：
1993-10-20
影响因子：
5.6
通讯作者：
OVERINGTON, JP
中科院分区：
文献类型：
--
作者：
JOHNSON, MS;OVERINGTON, JP
一个残基交换矩阵已被推导出来，是适合于比较的氨基酸序列。该矩阵基于在65组同源的结构对齐的三维结构（235种蛋白质）中观察到的207，795个氨基酸置换的列表。大多数数据来自结构比较，其中存在15%至40%的序列同一性。因此，一个评分矩阵，如这里设计的一个应该提供一个敏感的基础，比较氨基酸序列和氨基酸数据库中的同源序列的搜索。为了评估该矩阵的价值，我们与其他12个已发表的评分矩阵进行了比较分析，这些评分矩阵已用于蛋白质氨基酸序列的比对。我们发现，这里得到的矩阵是在比对意义，同源序列的检测和比对的准确性方面的更好的表演者之一。
A residue-exchange matrix has been derived that is suitable for comparison of amino acid sequences. This matrix is based on the tabulation of 207,795 amino acid replacements observed in 65 homologous sets of structurally aligned three-dimensional structures (235 proteins). The majority of the data is from structural comparisons where there is between 15 and 40% sequence identity. As a result, a scoring matrix such as the one devised here should provide a sensitive basis for the comparison of amino acid sequences and the search for homologous sequences in amino acid databases. In order to assess the value of this matrix we have made a comparative analysis with 12 other published scoring matrices that have been used for the alignment of protein amino acid sequences. We find that the matrix derived here is among the better performers in terms of alignment significance, detection of homologous sequences and the accuracy of alignments.