Constrained sequence alignment

Kun Mao Chao; Ross C. Hardison; Webb Miller

doi:10.1007/BF02460648

Constrained sequence alignment

Kun Mao Chao, Ross C. Hardison, Webb Miller

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

18 Scopus citations

Abstract

This paper presents a dynamic programming algorithm for aligning two sequeces when the alignment is constrained to lie between two arbitrary boundary lines in the dynamic programming matrix. For affine gap penalties, the algorithm requires only O(F) computation time and O(M+N) space, where F is the area of the feasible region and M and N are the sequence lengths. The result extends to concave gap penalties, with somewhat increased time and space bounds.

Original language	English (US)
Pages (from-to)	503-524
Number of pages	22
Journal	Bulletin of Mathematical Biology
Volume	55
Issue number	3
DOIs	https://doi.org/10.1007/BF02460648
State	Published - May 1993

All Science Journal Classification (ASJC) codes

Neuroscience(all)
Immunology
Mathematics(all)
Biochemistry, Genetics and Molecular Biology(all)
Environmental Science(all)
Pharmacology
Agricultural and Biological Sciences(all)
Computational Theory and Mathematics

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10.1007/BF02460648

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abstract = "This paper presents a dynamic programming algorithm for aligning two sequeces when the alignment is constrained to lie between two arbitrary boundary lines in the dynamic programming matrix. For affine gap penalties, the algorithm requires only O(F) computation time and O(M+N) space, where F is the area of the feasible region and M and N are the sequence lengths. The result extends to concave gap penalties, with somewhat increased time and space bounds.",

author = "Chao, {Kun Mao} and Hardison, {Ross C.} and Webb Miller",

note = "Funding Information: K.-M. C. and W. M. were supported in part by grant R01 LM05110 from the National Library of Medacine. R. C. H. was supported by PHS grant R01 DK27635",

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AU - Hardison, Ross C.

AU - Miller, Webb

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PY - 1993/5

Y1 - 1993/5

N2 - This paper presents a dynamic programming algorithm for aligning two sequeces when the alignment is constrained to lie between two arbitrary boundary lines in the dynamic programming matrix. For affine gap penalties, the algorithm requires only O(F) computation time and O(M+N) space, where F is the area of the feasible region and M and N are the sequence lengths. The result extends to concave gap penalties, with somewhat increased time and space bounds.

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Constrained sequence alignment

Abstract

All Science Journal Classification (ASJC) codes

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