On all-substrings alignment problems

Authors:
Wei Fu;Wing-Kai Hon;Wing-Kin Sung
Affiliations:
School of Computing, National University of Singapore, Singapore;Department of Computer Science and Information Systems, The University of Hong Kong, Hong Kong;School of Computing, National University of Singapore, Singapore
Venue:
COCOON'03 Proceedings of the 9th annual international conference on Computing and combinatorics
Year:
2003

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Abstract

Consider two strings A and B of lengths n and m respectively, with n ≪ m. The problem of computing global and local alignments between A and all m2 substrings of B can be solved by the classical Needleman-Wunsch and Smith-Waterman algorithms, respectively, which takes O(m2n) time and O(m2) space. This paper proposes faster algorithms that take O(mn2) time and O(mn) space. The improvement stems from a compact way to represent all the alignment scores.