Approximate string matching using compressed suffix arrays

  • Authors:

  • Trinh N. D. Huynh;Wing-Kai Hon;Tak-Wah Lam;Wing-Kin Sung

  • Affiliations:

  • School of Computing, National University of Singapore, Singapore;Department of Computer Science and Information Systems, The University of Hong Kong, Hong Kong;Department of Computer Science and Information Systems, The University of Hong Kong, Hong Kong;School of Computing, National University of Singapore, Singapore

  • Venue:
  • Theoretical Computer Science
  • Year:
  • 2006

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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 T is fixed and preprocessed into an indexing data structure so that any pattern query can be answered faster. We give a solution using an O(n log n) bits indexing data structure with O(|A|kmkċmax(k, log n) +occ) query time, where occ is the number of occurrences. The best previous result requires O(n log n) bits indexing data structure and gives O(|A|kmk+2 + occ) query time. Our solution also allows us to exploit compressed suffix arrays to reduce the indexing space to O(n) bits, while increasing the query time by an O(log n) factor only.