Mount David W
Cold Spring Harb Protoc. 2009 Jul;2009(7):pdb.top43. doi: 10.1101/pdb.top43.
Finding a global optimal alignment of more than two sequences that includes matches, mismatches, and gaps and that takes into account the degree of variation in all of the sequences at the same time is especially difficult. The dynamic programming algorithm used for optimal alignment of pairs of sequences can be extended to global alignment of three sequences, but for more than three sequences, only a small number of relatively short sequences may be analyzed. Thus, approximate methods are used for global sequence alignment. One class of these methods is progressive global alignment, which starts with an alignment of the most alike sequences and then builds an alignment by adding more sequences. This article introduces three programs that use progressive alignment methodology.
找到包含匹配、错配和空位且能同时考虑所有序列变异程度的两个以上序列的全局最优比对尤其困难。用于两个序列最优比对的动态规划算法可以扩展到三个序列的全局比对，但对于三个以上的序列，可能只能分析少量相对较短的序列。因此，近似方法用于全局序列比对。这类方法中的一类是渐进全局比对，它从最相似序列的比对开始，然后通过添加更多序列来构建比对。本文介绍了三个使用渐进比对方法的程序。
