Locating alignments with k differences for nucleotide and amino acid sequences

Gad M. Landau, Uzi Vishkin, Ruth Nussinov

Research output: Contribution to journalArticlepeer-review


Given two sequences, a pattern of length m, a text of length n and a positive integer k, we give two algorithms. The first finds all occurrences of the pattern in the text as long as these do not differ from each other by more than k differences. It runs in O(nk) time. The second algorithm finds all subsequence alignments between the pattern and the test with at most k differences. This algorithm runs in O(nmk) time, is very simple and easy to program.

Original languageEnglish
Pages (from-to)19-24
Number of pages6
Issue number1
StatePublished - Mar 1988
Externally publishedYes

Bibliographical note

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

ASJC Scopus subject areas

  • Computational Mathematics
  • Molecular Biology
  • Biochemistry
  • Statistics and Probability
  • Computer Science Applications
  • Computational Theory and Mathematics


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