Cache-oblivious index for approximate string matching

  • Authors:

  • Wing-Kai Hon;Tak-Wah Lam;Rahul Shah;Siu-Lung Tam;Jeffrey Scott Vitter

  • Affiliations:

  • Department of Computer Science, National Tsing Hua University, Taiwan;Department of Computer Science, The University of Hong Kong, Hong Kong;Department of Computer Science, Louisiana State University, LA, USA;Department of Computer Science, The University of Hong Kong, Hong Kong;Department of Electrical Engineering and Computer Science, Kansas University, KS, USA

  • Venue:
  • Theoretical Computer Science
  • Year:
  • 2011

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Abstract

This paper revisits the problem of indexing a text for approximate string matching. Specifically, given a text T of length n and a positive integer k, we want to construct an index of T such that for any input pattern P, we can find all its k-error matches in T efficiently. This problem is well-studied in the internal-memory setting. Here, we extend some of these recent results to external-memory solutions, which are also cache-oblivious. Our first index occupies O((nlog^kn)/B) disk pages and finds all k-error matches with O((|P|+occ)/B+log^knloglog"Bn) I/Os, where B denotes the number of words in a disk page. To the best of our knowledge, this index is the first external-memory data structure that does not require @W(|P|+occ+poly(logn)) I/Os. The second index reduces the space to O((nlogn)/B) disk pages, and the I/O complexity is O((|P|+occ)/B+log^k^(^k^+^1^)nloglogn).