A new algorithm for fast all-against-all substring matching

Authors:
Marina Barsky;Ulrike Stege;Alex Thomo;Chris Upton
Affiliations:
University of Victoria, Canada;University of Victoria, Canada;University of Victoria, Canada;University of Victoria, Canada
Venue:
SPIRE'06 Proceedings of the 13th international conference on String Processing and Information Retrieval
Year:
2006

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A graph approach to the threshold all-against-all substring matching problem

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Abstract

We present a new and efficient algorithm to solve the ’threshold all vs. all’ problem, which involves searching of two strings (with length N and M respectively) for finding all maximal approximate matches of length at least S and with up to K differences. The algorithm is based on a novel graph model, and it solves the problem in time O(NMK2).