ANALYSIS OF AMINO-ACID SUBSTITUTION DURING DIVERGENT EVOLUTION - THE 400 BY 400 DIPEPTIDE SUBSTITUTION MATRIX
ANALYSIS OF AMINO-ACID SUBSTITUTION DURING DIVERGENT EVOLUTION - THE 400 BY 400 DIPEPTIDE SUBSTITUTION MATRIX
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DOI：
10.1006/bbrc.1994.1255
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发表时间：
1994-03-15
影响因子：
3.1
通讯作者：
BENNER, SA
中科院分区：
文献类型：
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作者：
GONNET, GH;COHEN, MA;BENNER, SA
大多数分析蛋白质序列发散进化的正式方法都假设一个马尔可夫模型，其中多肽链上的第i位独立于第i+1位进行氨基酸取代。从蛋白质序列数据库的详尽匹配中获得的大量对齐的同源序列对使得从经验上检验这一假设成为可能。我们已经构建了一个400 × 400的矩阵，该矩阵报告了经历分化进化的蛋白质中所有对二肽相互转化的经验概率。如果蛋白质序列中相邻位置的取代是独立的，那么将这些概率与预期的概率进行比较，就会发现通过打破这一假设而产生的有趣模式。其中一些在从同源蛋白序列的保护和变异模式中提取构象信息是有用的。(C) 1994学术出版社，Inc.
Most formal methods for analyzing the divergent evolution of protein sequences assume a Markov model where position i in a polypeptide chain undergoes amino acid substitution independently from position i+1. The large number of aligned homologous sequence pairs available from the exhaustive matching of the protein sequence database makes it possible to examine this assumption empirically. We have constructed a 400 by 400 matrix that reports empirical probabilities for the interconversion of all pairs of dipeptides in proteins undergoing divergent evolution. Comparison of these probabilities with those expected if substitution at adjacent positions in a protein sequence were independent reveals interesting patterns that arise through the breakdown of this assumption. Several of these are useful in extracting conformational information from patterns of conservation and variation in homologous protein sequences. (C) 1994 Academic Press, Inc.