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

Gad M. Landau; Uzi Vishkin; Ruth Nussinov

doi:10.1016/S0022-5193(87)80153-4

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 journal › Article › peer-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 language	English
Pages (from-to)	483-490
Number of pages	8
Journal	Journal of Theoretical Biology
Volume	126
Issue number	4
DOIs	https://doi.org/10.1016/S0022-5193(87)80153-4
State	Published - 21 Jun 1987
Externally published	Yes

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
General Biochemistry, Genetics and Molecular Biology
General Immunology and Microbiology
General Agricultural and Biological Sciences
Applied Mathematics

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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.",

author = "Landau, {Gad M.} and Uzi Vishkin and Ruth Nussinov",

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.",

year = "1987",

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doi = "10.1016/S0022-5193(87)80153-4",

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AU - Vishkin, Uzi

AU - Nussinov, Ruth

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PY - 1987/6/21

Y1 - 1987/6/21

N2 - 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.

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

Abstract

Bibliographical note

ASJC Scopus subject areas

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