On-line approximate string matching with bounded errors

Marcos Kiwi, Gonzalo Navarro, Claudio Telha*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

We introduce a new dimension to the widely studied on-line approximate string matching problem, by introducing an error threshold parameter ∈ so that the algorithm is allowed to miss occurrences with probability ∈. This is particularly appropriate for this problem, as approximate searching is used to model many cases where exact answers are not mandatory. We show that the relaxed version of the problem allows us breaking the average-case optimal lower bound of the classical problem, achieving average case O(n log σ m/m) time with any ∈ = poly(k/m), where n is the text size, m the pattern length, k the number of differences for edit distance, and σ the alphabet size. Our experimental results show the practicality of this novel and promising research direction. Finally, we extend the proposed approach to the multiple approximate string matching setting, where the approximate occurrence of r patterns are simultaneously sought. Again, we can break the average-case optimal lower bound of the classical problem, achieving average case O(n logσ (rm)/m) time with any ∈ = poly(k/m).

Original languageEnglish
Pages (from-to)6359-6370
Number of pages12
JournalTheoretical Computer Science
Volume412
Issue number45
DOIs
StatePublished - 21 Oct 2011
Externally publishedYes

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