Johnson M S, Doolittle R F
J Mol Evol. 1986;23(3):267-78. doi: 10.1007/BF02115583.
We describe an algorithm for the concurrent comparison of three or more amino acid sequences. The basis of the approach is a progressive evaluation of selected segments from each sequence. Only a small subset of all possible segments from each sequence is compared, and a minimum of information is retained for the trace-back of the alignment. As a result, this method has the advantage of being both rapid and minimally consumptive of computer memory when constructing an alignment. This being the case, there are no practical limits on the length of sequences that may be aligned. A computer program for the alignment of three sequences is described, and this method is compared with two three-sequence extensions of the Needleman and Wunsch variety, including a recently published approach. In addition, we have made simultaneous alignments of sets of four and five sequences with this selected-segment method.
我们描述了一种用于同时比较三个或更多氨基酸序列的算法。该方法的基础是对每个序列中选定片段进行逐步评估。每个序列中所有可能片段的只有一小部分被比较，并且为比对的回溯保留最少的信息。因此，该方法在构建比对时具有快速且计算机内存消耗最小的优点。在这种情况下，可比对的序列长度没有实际限制。描述了一个用于比对三个序列的计算机程序，并将该方法与Needleman和Wunsch方法的两种三序列扩展方法（包括最近发表的一种方法）进行了比较。此外，我们使用这种选定片段方法同时比对了四个和五个序列的集合。
