Locating alignments with k differences for nucleotide and amino acid sequences

Gad M. Landau; Uzi Vishkin; Ruth Nussinov

doi:10.1093/bioinformatics/4.1.19

Locating alignments with k differences for nucleotide and amino acid sequences

Gad M. Landau, Uzi Vishkin, Ruth Nussinov

Research output: Contribution to journal › Article › peer-review

Abstract

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 language	English
Pages (from-to)	19-24
Number of pages	6
Journal	Bioinformatics
Volume	4
Issue number	1
DOIs	https://doi.org/10.1093/bioinformatics/4.1.19
State	Published - Mar 1988
Externally published	Yes

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

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

Access to Document

10.1093/bioinformatics/4.1.19

Cite this

@article{40e3b0798eb54faaa05657c694f5975e,

title = "Locating alignments with k differences for nucleotide and amino acid sequences",

abstract = "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.",

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

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.",

year = "1988",

month = mar,

doi = "10.1093/bioinformatics/4.1.19",

language = "English",

volume = "4",

pages = "19--24",

journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "1",

}

TY - JOUR

T1 - Locating alignments with k differences for nucleotide and amino acid sequences

AU - Landau, Gad M.

AU - Vishkin, Uzi

AU - Nussinov, Ruth

N1 - 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.

PY - 1988/3

Y1 - 1988/3

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=0023984869&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/4.1.19

DO - 10.1093/bioinformatics/4.1.19

M3 - Article

C2 - 3382993

AN - SCOPUS:0023984869

SN - 1367-4803

VL - 4

SP - 19

EP - 24

JO - Bioinformatics

JF - Bioinformatics

IS - 1

ER -

Locating alignments with k differences for nucleotide and amino acid sequences

Abstract

Bibliographical note

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this