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Digitale Medien

Constrained sequence alignment (1993)

Chao, Kun-Mao ; Hardison, Ross C. ; Miller, Webb

Springer

Bulletin of mathematical biology 55 (1993), S. 503-524

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Details

ISSN: 1522-9602

Quelle: Springer Online Journal Archives 1860-2000

Thema: Biologie , Mathematik

Notizen: 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 onlyO(F) computation time andO(M+N) space, whereF is the area of the feasible region andM andN are the sequence lengths. The result extends to concave gap penalties, with somewhat increased time and space bounds.

Materialart: Digitale Medien

URL: http://dx.doi.org/10.1007/BF02460648

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