Abstract
Motivated by applications in bioinformatics, in what follows, we extend the notion of gapped strings to elastic-degenerate strings. An elastic-degenerate string can been seen as an ordered collection of solid (standard) strings interleaved by elastic-degenerate symbols; each such symbol corresponds to a set of two or more variable-length solid strings. In this article, we present an algorithm for solving the pattern matching problem with a solid pattern and an elastic-degenerate text running in \(\mathcal {O}(N+\alpha \gamma mn)\) time; where m is the length of the pattern; n and N are the length and total size of the elastic-degenerate text, respectively; \(\alpha \) and \(\gamma \) are parameters, respectively representing the maximum number of strings in any elastic-degenerate symbol of the text and the maximum number of elastic-degenerate symbols spanned by any occurrence of the pattern in the text. The space used by the proposed algorithm is \(\mathcal {O}(N)\).
This work was partially supported by the British Council funded INSPIRE Project.
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Iliopoulos, C.S., Kundu, R., Pissis, S.P. (2017). Efficient Pattern Matching in Elastic-Degenerate Texts. In: Drewes, F., Martín-Vide, C., Truthe, B. (eds) Language and Automata Theory and Applications. LATA 2017. Lecture Notes in Computer Science(), vol 10168. Springer, Cham. https://doi.org/10.1007/978-3-319-53733-7_9
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