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

Abstract

We present a novel graph model and an efficient algorithm for solving the "threshold all against all" problem, which involves searching two strings (with length M and N , respectively) for all maximal approximate substring matches of length at least S, with up to K differences. Our algorithm solves the problem in time O(MNK 3 ), which is a considerable improvement over the previous known bound for this problem. We also provide experimental evidence that, in practice, our algorithm exhibits a better performance than its worst-case running time. ACM Reference Format:Barsky, M., Stege, U., Thomo, A., Upton, C. 2008. A graph approach to the threshold all-against-all substring matching problem. ACM J.

JaPaFi: A Novel Program for the Identification of Highly Conserved DNA Sequences

“…In order to locate the approximate matches, the program performs two computations. In the first part, called Iterative Filtering, each pair of sequences is processed using the modification of the APBT algorithm described in [ 21 ]. The original APBT finds all approximate matches of length of at least S and with up to K differences in two strings.…”