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Faster Approximate Elastic-Degenerate String Matching - Part A.

Authors: Solon P. Pissis; Jakub Radoszewski; Wiktor Zuba;

Faster Approximate Elastic-Degenerate String Matching - Part A.

Abstract

An elastic-degenerate (ED) string T is a sequence T = T[1] · · · T[n] of n finite sets of strings. The cardinality m of T is the total number of strings in T[i], for all i ∈ [1 . . n]. The size N of T is the total length of all m strings of T. ED strings have been introduced to represent a set of closely-related DNA sequences. Let P = P[1 . . p] be a pattern of length p and k > 0 be an integer. We consider the problem of k-Approximate ED String Matching (EDSM): searching k-approximate occurrences of P in the language of T. We call k-Approximate EDSM under the Hamming distance, k-Mismatch EDSM; and we call k-Approximate EDSM under edit distance, k-Edit EDSM. Bernardini et al. (Theoretical Computer Science, 2020) showed a simple O(kmp + kN)-time algorithm for k-Mismatch EDSM and an O(k2mp + kN)-time algorithm for k-Edit EDSM. We improve the dependency on k in both results, obtaining an Õ(k2/3mp +√kN)-time algorithm for k-Mismatch EDSM and an Õ(kmp + kN)-time algorithm for k-Edit EDSM. Bernardini et al. (Theory of Computing Systems, 2024) presented several algorithms for 1-Approximate EDSM working in Õ(np2 + N) time. They have also left the possibility to generalize these solutions for k > 1 as an open problem. We improve the runtime of their solution for 1-Mismatch and 1-Edit EDSM from Õ(np2 + N) to O(np2 + N). We further show algorithms for k-Approximate EDSM for the Hamming and edit distances working in Õ(np2 + N) time, for any constant k > 0. Finally, we show how our techniques can be applied to improve upon the complexity of the k-Approximate ED String Intersection and k-Approximate Doubly EDSM problems that were introduced very recently by Gabory et al. (Information and Computation, 2025).

Countries
Germany, Netherlands
Keywords

approximate string matching, Hamming distance, edit distance, ED string, ddc: ddc:004

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average
Green