Approximate string matching using compressed suffix arrays

Abstract

Let T be a text of length n and P be a pattern of length m, both strings over a fixed finite alphabet A. The k-difference (k-mismatch, respectively) problem is to find all occurrences of P in T that have edit distance (Hamming distance, respectively) at most k from P. In this paper we investigate a well-studied case in which k = 1 and T is fixed and preprocessed into an indexing data structure so that any pattern query can be answered faster [16-19]. This paper gives a solution using O(n) bits indexing data structure with O(m log2 n) query time. To the best of our knowledge, this is the first result which requires linear indexing space. The results can be extended for the fc-difference problem with k ≥ 1. © Springer-Verlag 2004.