Sequence Alignment Algorithms for Run-Length-Encoded Strings

Authors:
Guan Shieng Huang;Jia Jie Liu;Yue Li Wang
Affiliations:
Department of Computer Science and Information Engineering, National Chi Nan University, Taiwan;Department of Information Management, Shih Hsin University, Taiwan;Department of Computer Science and Information Engineering, National Chi Nan University, Taiwan
Venue:
COCOON '08 Proceedings of the 14th annual international conference on Computing and Combinatorics
Year:
2008

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Abstract

A unified framework is applied to solving various sequence comparison problems for run-length encoded strings. All of these algorithms take O( min {mn茂戮驴,m茂戮驴n}) time and O( max {m,n}) space, for two strings of lengths mand n, with m茂戮驴 and n茂戮驴 runs, respectively. We assume the linear-gap model and make no assumption on the scoring matrices, which maximizes the applicability of these algorithms. The trace (i.e., the way to align two strings) of an optimal solution can also be recovered within the same time and space bounds.