Bit-parallel Computation for String Alignment ⁄

One of the most important ideas in data mining is alignment of two strings. This idea is based on a distance on strings and the most popular and simple one is the edit distance. For two strings of lengths m and n, the alignment and the edit distance is computed in O(mn) time by dynamic programming approach. Bit-parallelism can speed-up the computation of the edit distance w times, where w is the word size of a computer, however this parallelism can not be applied straightforwardly to computing the alignment. This paper proposes a bit-parallel algorithm to compute all the possible alignments.