An efficient string matching algorithm with k differences for nudeotide and amino acid sequences

Gad M. Landau, Uzi Vishkin, Ruth Nussinov

Research output: Contribution to journalArticlepeer-review

Abstract

There are a few algorithms designed to solve the problem of the optimal alignment of one sequence, the pattern, of length m, with another, longer sequence the text, of length n These algorithms allow mismatches, deletions and insertions. Algorithms to date run in 0(mn) time. Let us define an integer. k, which is the maximal number of differences allowed We present a simple algorithm showing that sequences can be optimally aligned in O(k2) time. For long sequences the gain factor over the currently used algorithms is very large.

Original languageEnglish
Pages (from-to)31-46
Number of pages16
JournalNucleic Acids Research
Volume14
Issue number1
DOIs
StatePublished - 10 Jan 1986
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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