Felsenstein J, Sawyer S, Kochin R
Nucleic Acids Res. 1982 Jan 11;10(1):133-9. doi: 10.1093/nar/10.1.133.
A method of computing the fraction of matches between two nucleic acid sequences at all possible alignments is described. It makes use of the Fast Fourier Transform. It should be particularly efficient for very long sequences, achieving its result in a number of operations proportional to n ln n, where n is the length of the longer of the two sequences. Though the objective achieved is of limited interest, this method will complement algorithms for efficiently finding the longest matching parts of two sequences, and is faster than existing algorithms for finding matches allowing deletions and insertions. A variety of economies can be achieved by this Fast Fourier Transform technique in matching multiple sequences, looking for complementarity rather than identity, and matching the same sequences both in forward and reversed orientations.
本文描述了一种计算两个核酸序列在所有可能比对情况下匹配分数的方法。该方法利用了快速傅里叶变换。对于非常长的序列，它应该特别高效，在与n ln n成正比的操作次数内得到结果，其中n是两个序列中较长序列的长度。尽管所实现的目标兴趣有限，但该方法将补充用于高效找到两个序列最长匹配部分的算法，并且比现有的允许删除和插入的匹配查找算法更快。通过这种快速傅里叶变换技术，可以在匹配多个序列、寻找互补性而非同一性以及正向和反向匹配相同序列方面实现多种节省。
