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A Fast Algorithm for the Optimal Alignment of Three Strings. Lloyd Allison,

Summary: A Fast Algorithm for the Optimal Alignment of Three Strings.
Lloyd Allison,
Department of Computer Science,
Monash University,
Australia 3168.
email: lloyd@cs.monash.edu.au
Partly supported by an Australian Research Council grant.
J. Theor. Biol. 164(2) 261­269 Sept 1993

Fast Algorithm for Alignment of Three Strings. ­2­
Abstract. Ukkonen's (pair­wise) string alignment technique is extended to the problem of finding an
optimal alignment for three strings. The resulting algorithm has worst­case time­complexity O(nd 2 ) and
space­complexity O(d 3 ), where the string lengths are ”n and d is the three­way edit­distance based on tree­
costs. In practice the algorithm usually runs in O(n+d 3 ) time. The algorithm is particularly fast when the
strings are similar in which case d< Three­way alignment is an important special case in string alignment. Each internal node in an
unrooted, binary evolutionary­tree has three neighbours. The algorithm presented can be used as an
iterative step in a heuristic multiple­alignment program for more than three strings.
Keywords: alignment, edit­distance, multiple­alignment, sequence, string, three.


Source: Allison, Lloyd - Caulfield School of Information Technology, Monash University


Collections: Computer Technologies and Information Sciences