Identifying periodic occurences of a template with applications to protein structure

Vincent A. Fischetti; Gad M. Landau; Peter H. Sellers; Jeanette P. Schmidt

doi:10.1016/0020-0190(93)90245-5

Identifying periodic occurences of a template with applications to protein structure

Vincent A. Fischetti, Gad M. Landau, Peter H. Sellers, Jeanette P. Schmidt

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

Abstract

Consider a template P of size m in which each character matches many different characters with various degrees of perfection. Given a text T of size n, we present a simple and practical algorithm that finds the substring of T, which best matches some substring of Pⁿ (Pⁿ is the concatenation of an arbitrary number of copies of P). The algorithm produces the matched pair and their alignment in O(mn) time.

Original language	English
Pages (from-to)	11-18
Number of pages	8
Journal	Information Processing Letters
Volume	45
Issue number	1
DOIs	https://doi.org/10.1016/0020-0190(93)90245-5
State	Published - 25 Jan 1993
Externally published	Yes

Keywords

Design of algorithms
computational biology
string matching

ASJC Scopus subject areas

Theoretical Computer Science
Signal Processing
Information Systems
Computer Science Applications

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10.1016/0020-0190(93)90245-5

Cite this

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abstract = "Consider a template P of size m in which each character matches many different characters with various degrees of perfection. Given a text T of size n, we present a simple and practical algorithm that finds the substring of T, which best matches some substring of Pn (Pn is the concatenation of an arbitrary number of copies of P). The algorithm produces the matched pair and their alignment in O(mn) time.",

keywords = "Design of algorithms, computational biology, string matching",

author = "Fischetti, {Vincent A.} and Landau, {Gad M.} and Sellers, {Peter H.} and Schmidt, {Jeanette P.}",

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AU - Fischetti, Vincent A.

AU - Landau, Gad M.

AU - Sellers, Peter H.

AU - Schmidt, Jeanette P.

PY - 1993/1/25

Y1 - 1993/1/25

N2 - Consider a template P of size m in which each character matches many different characters with various degrees of perfection. Given a text T of size n, we present a simple and practical algorithm that finds the substring of T, which best matches some substring of Pn (Pn is the concatenation of an arbitrary number of copies of P). The algorithm produces the matched pair and their alignment in O(mn) time.

AB - Consider a template P of size m in which each character matches many different characters with various degrees of perfection. Given a text T of size n, we present a simple and practical algorithm that finds the substring of T, which best matches some substring of Pn (Pn is the concatenation of an arbitrary number of copies of P). The algorithm produces the matched pair and their alignment in O(mn) time.

KW - Design of algorithms

KW - computational biology

KW - string matching

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Identifying periodic occurences of a template with applications to protein structure

Abstract

Keywords

ASJC Scopus subject areas

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