Murata M, Richardson J S, Sussman J L
Proc Natl Acad Sci U S A. 1985 May;82(10):3073-7. doi: 10.1073/pnas.82.10.3073.
Currently there are several computer algorithms available for aligning two biological sequences. When more than two sequences are to be aligned, however, pairwise comparisons using these methods rarely lead to a consistent alignment of the sequences. One obvious solution to this problem is to compare all the sequences simultaneously. Here we present an algorithm for the simultaneous comparison of three biological sequences. The algorithm is an extension of the method developed by S. B. Needleman and C. D. Wunsch, but it decreases the almost prohibitively long computing time required by a direct naive extension to a practical level: it takes time proportional to the cube of the mean sequence length, in comparison to the fifth power time taken by the direct extension. Simultaneous comparison not only gives a consistent alignment of the three sequences, but it could also reveal homologous residues in the sequences that might be overlooked by the pairwise comparisons. As an example of the application of the algorithm, three copper-containing proteins, plastocyanin, stellacyanin, and cucumber basic blue protein, are compared.
目前有几种计算机算法可用于比对两个生物序列。然而，当要比对的序列超过两个时，使用这些方法进行成对比较很少能得到序列的一致比对。解决这个问题的一个明显方法是同时比较所有序列。在这里，我们提出一种用于同时比较三个生物序列的算法。该算法是S. B. 尼德曼和C. D. 温施开发的方法的扩展，但它将直接朴素扩展所需的几乎长得令人望而却步的计算时间减少到了实际可行的水平：它所花费的时间与平均序列长度的立方成正比，相比之下，直接扩展所花费的时间是平均序列长度的五次方。同时比较不仅能给出三个序列的一致比对，还能揭示序列中可能被成对比较忽略的同源残基。作为该算法应用的一个例子，对三种含铜蛋白质，即质体蓝素、星蓝蛋白和黄瓜碱性蓝蛋白进行了比较。
