An efficient string matching algorithm with K substitutions for nucleotide and amino acid sequences

Gad M. Landau, Uzi Vishkin, Ruth Nussinov

Research output: Contribution to journalArticlepeer-review

Abstract

Given a text of length n, a pattern of length m and an integer k, we present an algorithm for finding all occurrences of the pattern in the text, each with at most k substitutions. The algorithm runs in O(k(m log m + n)) time, and requires O(nk) space. This algorithm has direct implications for nucleotide and amino acid sequence comparisons.

Original languageEnglish
Pages (from-to)483-490
Number of pages8
JournalJournal of Theoretical Biology
Volume126
Issue number4
DOIs
StatePublished - 21 Jun 1987
Externally publishedYes

Bibliographical note

Funding Information:
U. Vishkin has been supported by NSF grants NSF-CCR-8615337 and NSF-DCR-8413359, ONR grant N00014-85-K-0046. U. Vishkin and G. M. Landau have been supported by the Applied Mathematical Sciences subprogram of the Office of Energy Research, U.S. Department of Energy, under contract number DE-AC02-76ER03077.

ASJC Scopus subject areas

  • Statistics and Probability
  • Modeling and Simulation
  • Biochemistry, Genetics and Molecular Biology (all)
  • Immunology and Microbiology (all)
  • Agricultural and Biological Sciences (all)
  • Applied Mathematics

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