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Journal Articles Information and Computation Year : 2021

Efficient pattern matching in elastic-degenerate strings

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Abstract

In this paper, we extend the notion of gapped strings to elastic-degenerate strings. An elastic-degenerate string can been seen as an ordered collection of k > 1 seeds (substrings/subpatterns) interleaved by elastic-degenerate symbols such that each elastic-degenerate symbol corresponds to a set of two or more variable length strings. Here, we present an algorithm for solving the pattern matching problem with (solid) pattern and elastic-degenerate text, running in O(N +αγnm) time; where m is the length of the given pattern; n and N are the length and total size of the given elastic-degenerate text, respectively; α and γ are small constants, respectively representing the maximum number of strings in any elastic-degenerate symbol of the text and the largest number of elastic-degenerate symbols spanned by any occurrence of the pattern in the text. The space used by the algorithm is linear in the size of the input for a constant number of elastic-degenerate symbols in the text; α and γ are so small in real applications that the algorithm is expected to work very efficiently in practice.
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Dates and versions

hal-03498329 , version 1 (21-12-2021)

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Costas S Iliopoulos, Ritu Kundu, Solon P Pissis. Efficient pattern matching in elastic-degenerate strings. Information and Computation, 2021, 279, pp.1-13. ⟨10.1016/j.ic.2020.104616⟩. ⟨hal-03498329⟩

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