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Constructing Strings Avoiding Forbidden Substrings
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In: CPM 2021 - 32nd Annual Symposium on Combinatorial Pattern Matching ; https://hal.inria.fr/hal-03395386 ; CPM 2021 - 32nd Annual Symposium on Combinatorial Pattern Matching, Jul 2021, Wroclaw, Poland. pp.1-18 (2021)
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Bidirectional String Anchors: A New String Sampling Mechanism ...
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Longest Unbordered Factor in Quasilinear Time
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Kociumaka, Tomasz; Kundu, Ritu; Mohamed, Manal. - : Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, 2018. : LIPIcs - Leibniz International Proceedings in Informatics. 29th International Symposium on Algorithms and Computation (ISAAC 2018), 2018
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Longest Common Prefixes with $k$-Errors and Applications ...
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Optimal Computation of Overabundant Words ...
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Abstract:
The observed frequency of the longest proper prefix, the longest proper suffix, and the longest infix of a word $w$ in a given sequence $x$ can be used for classifying $w$ as avoided or overabundant. The definitions used for the expectation and deviation of $w$ in this statistical model were described and biologically justified by Brendel et al. (J Biomol Struct Dyn 1986). We have very recently introduced a time-optimal algorithm for computing all avoided words of a given sequence over an integer alphabet (Algorithms Mol Biol 2017). In this article, we extend this study by presenting an $\mathcal{O}(n)$-time and $\mathcal{O}(n)$-space algorithm for computing all overabundant words in a sequence $x$ of length $n$ over an integer alphabet. Our main result is based on a new non-trivial combinatorial property of the suffix tree $\mathcal{T}$ of $x$: the number of distinct factors of $x$ whose longest infix is the label of an explicit node of $\mathcal{T}$ is no more than $3n-4$. We further show that the ...
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Keyword:
Data Structures and Algorithms cs.DS; FOS Computer and information sciences
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URL: https://dx.doi.org/10.48550/arxiv.1705.03385 https://arxiv.org/abs/1705.03385
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Efficient Index for Weighted Sequences
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Barton, Carl; Kociumaka, Tomasz; Pissis, Solon P.. - : Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, 2016. : LIPIcs - Leibniz International Proceedings in Informatics. 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016), 2016
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Linear-time computation of minimal absent words using suffix array
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Order-Preserving Suffix Trees and Their Algorithmic Applications ...
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