Fast bit-vector algorithms for approximate string matching under indel distance

Heikki Hyyrö, Yoan Pinzon, Ayumi Shinohara

Research output: Contribution to journalConference article

6 Citations (Scopus)

Abstract

The approximate string matching problem is to find all locations at which a query p of length m matches a substring of a text t of length n with at most k differences (insertions, deletions, substitutions). The fastest solutions in practice for this problem are the bit-parallel NFA simulation algorithms of Wu & Manber [4] and Baeza-Yates & Navarro [1], and the bit-parallel dynamic programming algorithm of Myers [3]. In this paper we present modified versions of these algorithms to deal with the restricted case where only insertions and deletions (called indel for short) are permitted. We also show test results with the algorithms.

Original languageEnglish
Pages (from-to)380-384
Number of pages5
JournalLecture Notes in Computer Science
Volume3381
Publication statusPublished - 2005 Sep 9
Externally publishedYes
Event31st Conference on Current Trends in Theory and Practice of Computer Science - Liptovsky Jan, Slovakia
Duration: 2005 Jan 222005 Jan 28

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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