A Note on Bit-Parallel Alignment Computation

Abstract. The edit distance between strings A and B is defined as the minimum number of edit operations needed in converting A into B or vice versa. Typically the allowed edit operations are one or more of the following: an insertion, a deletion or a substitution of a character, or a transposition between two adjacent characters. Simple edit distance allows the first two operation types, Levenshtein edit distance the first three, and Damerau distance all four. There exist very efficient O( m/w n) bit-parallel algorithms for computing each of these three distances, where m is the length of A, n is the length of B, and w is the computed word size. In this paper we discuss augmenting the bitparallel algorithms to recover an optimal alignment between A and B. Such an alignment depicts how to transform A into B by using ed(A, B) operations, where ed(A, B) is the used edit distance (one of the three mentioned above). Previously Iliopoulos and Pinzon have given such an algorithm for the longe...

• Type: Conference
• Year: 2004
• Where: STRINGOLOGY
• Authors: Heikki Hyyrö
• Keywords: Edit Distance, Edit Operations, Simple Edit Distance, STRINGOLOGY 2004, STRINGOLOGY 2008