Finding gapped palindromes online

Yuta Fujishige, Michitaro Nakamura, Shunsuke Inenaga, Hideo Bannai, Masayuki Takeda

Research output: Chapter in Book/Report/Conference proceedingConference contribution

6 Citations (Scopus)

Abstract

A string s is said to be a gapped palindrome iff s = xyxRfor some strings x, y such that |x| ≥ 1, |y| ≥ 2, and xR denotes the reverse image of x.In this paper we consider two kinds of gapped palindromes, and present efficient online algorithms to compute these gapped palindromes occurring in a string.First, we show an online algorithm to find all maximal g-gapped palindromes with fixed gap length g ≥ 2 in a string of length n in O(n log σ) time and O(n) space, where σ is the alphabet size.Second, we show an online algorithm to find all maximal lengthconstrained gapped palindromes with arm length at least A ≥ 1 and gap length in range [gmin, gmax] in O (formula presented) time and O(n) space.We also show that if A is a constant, then there exists a string of length n which contains Ω(n(gmax− gmin)) maximal LCGPs, which implies we cannot hope for a significant speed-up in the worst case.

Original languageEnglish
Title of host publicationCombinatorial Algorithms - 27th International Workshop, IWOCA 2016, Proceedings
EditorsVeli Mäkinen, Simon J. Puglisi, Leena Salmela
PublisherSpringer Verlag
Pages191-202
Number of pages12
ISBN (Print)9783319445427
DOIs
Publication statusPublished - Jan 1 2016
Event27th International Workshop on Combinatorial Algorithms, IWOCA 2016 - Helsinki, Finland
Duration: Aug 17 2016Aug 19 2016

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume9843 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other27th International Workshop on Combinatorial Algorithms, IWOCA 2016
CountryFinland
CityHelsinki
Period8/17/168/19/16

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All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Fujishige, Y., Nakamura, M., Inenaga, S., Bannai, H., & Takeda, M. (2016). Finding gapped palindromes online. In V. Mäkinen, S. J. Puglisi, & L. Salmela (Eds.), Combinatorial Algorithms - 27th International Workshop, IWOCA 2016, Proceedings (pp. 191-202). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9843 LNCS). Springer Verlag. https://doi.org/10.1007/978-3-319-44543-4_15