New bit-parallel indel-distance algorithm

Heikki Hyyrö, Yoan Pinzon, Ayumi Shinohara

Research output: Contribution to journalConference articlepeer-review

2 Citations (Scopus)

Abstract

The task of approximate string matching is to find all locations at which a pattern string p of length m matches a substring of a text string t of length n with at most k differences. It is common to use Levenshtein distance [5], which allows the differences to be single-character insertions, deletions, substitutions. Recently, in [3], the IndelMYE, IndelWM and IndelBYN algorithms where introduced as modified version of the bit-parallel algorithms of Myers [6], Wu&Manber [10] and Baeza-Yates&Navarro [1], respectively. These modified versions where made to support the indel distance (only single-character insertions and/or deletions are allowed). In this paper we present an improved version of IndelMYE that makes a better use of the bit-operations and runs 24.5 percent faster in practice. In the end we present a complete set of experimental results to support our findings.

Original languageEnglish
Pages (from-to)380-390
Number of pages11
JournalLecture Notes in Computer Science
Volume3503
DOIs
Publication statusPublished - 2005
Externally publishedYes
Event4th International Workshop on Experimental and Efficient Algorithms, WEA 2005 - Santorini Island, Greece
Duration: 2005 May 102005 May 13

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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