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All fields Title Creator / Publisher Keyword Year AND OR AND NOT All fields Title Creator / Publisher Keyword Year AND OR AND NOT All fields Title Creator / Publisher Keyword Year AND OR AND NOT All fields Title Creator / Publisher Keyword Year AND OR AND NOT All fields Title Creator / Publisher Keyword Year Sort by creator [A → Z]' creator [Z → A]' publishing year ↑ (asc)' publishing year ↓ (desc)' title [A → Z]' title [Z → A]' Simple Search Hits 1 – 19 of 19 1 Constructing Strings Avoiding Forbidden Substrings Bernardini, Giulia; Marchetti-Spaccamela, Alberto; Pissis, Solon P.... 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) BASE Show details 2 String Sampling with Bidirectional String Anchors ... Loukides, Grigorios; Pissis, Solon P.; Sweering, Michelle. - : arXiv, 2021 BASE Show details 3 Faster Algorithms for Longest Common Substring ... Charalampopoulos, Panagiotis; Kociumaka, Tomasz; Pissis, Solon P.. - : Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021 BASE Show details 4 Constructing Strings Avoiding Forbidden Substrings ... Bernardini, Giulia; Marchetti-Spaccamela, Alberto; Pissis, Solon P.. - : Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021 BASE Show details 5 Faster Algorithms for Longest Common Substring ... Charalampopoulos, Panagiotis; Kociumaka, Tomasz; Pissis, Solon P.. - : arXiv, 2021 BASE Show details 6 Bidirectional String Anchors: A New String Sampling Mechanism ... Loukides, Grigorios; Pissis, Solon P.. - : Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021 BASE Show details 7 Unary Words Have the Smallest Levenshtein k-Neighbourhoods Charalampopoulos, Panagiotis; Pissis, Solon P.; Radoszewski, Jakub. - : LIPIcs - Leibniz International Proceedings in Informatics. 31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020), 2020 BASE Show details 8 Longest Common Substring Made Fully Dynamic Amir, Amihood; Charalampopoulos, Panagiotis; Pissis, Solon P.. - : Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, 2019. : LIPIcs - Leibniz International Proceedings in Informatics. 27th Annual European Symposium on Algorithms (ESA 2019), 2019 BASE Show details 9 Longest Unbordered Factor in Quasilinear Time 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 BASE Show details 10 Longest Common Prefixes with $k$-Errors and Applications ... Ayad, Lorraine A. K.; Charalampopoulos, Panagiotis; Iliopoulos, Costas S.. - : arXiv, 2018 BASE Show details 11 Longest Unbordered Factor in Quasilinear Time ... Kociumaka, Tomasz; Kundu, Ritu; Mohamed, Manal. - : Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik GmbH, Wadern/Saarbruecken, Germany, 2018 BASE Show details 12 Longest Unbordered Factor in Quasilinear Time ... Kociumaka, Tomasz; Kundu, Ritu; Mohamed, Manal. - : arXiv, 2018 BASE Show details 13 Optimal Computation of Overabundant Words Almirantis, Yannis; Charalampopoulos, Panagiotis; Gao, Jia; Iliopoulos, Costas S.; Mohamed, Manal; Pissis, Solon P.; Polychronopoulos, Dimitris. - : Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, 2017. : LIPIcs - Leibniz International Proceedings in Informatics. 17th International Workshop on Algorithms in Bioinformatics (WABI 2017), 2017 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 O(n)-time and 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 T of x: the number of distinct factors of x whose longest infix is the label of an explicit node of T is no more than 3n-4. We further show that the presented algorithm is time-optimal by proving that O(n) is a tight upper bound for the number of overabundant words. Finally, we present experimental results, using both synthetic and real data, which justify the effectiveness and efficiency of our approach in practical terms. Keyword: avoided words; Data processing Computer science; DNA sequence analysis; overabundant words; suffix tree URN: urn:nbn:de:0030-drops-76468 URL: https://drops.dagstuhl.de/opus/volltexte/2017/7646/ https://doi.org/10.4230/LIPIcs.WABI.2017.4 BASE Hide details 14 Optimal Computation of Overabundant Words ... Almirantis, Yannis; Charalampopoulos, Panagiotis; Gao, Jia. - : Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik GmbH, Wadern/Saarbruecken, Germany, 2017 BASE Show details 15 Optimal Computation of Overabundant Words ... Almirantis, Yannis; Charalampopoulos, Panagiotis; Gao, Jia. - : arXiv, 2017 BASE Show details 16 Efficient Index for Weighted Sequences 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 BASE Show details 17 Optimal Computation of Avoided Words ... Almirantis, Yannis; Charalampopoulos, Panagiotis; Gao, Jia. - : arXiv, 2016 BASE Show details 18 Linear-time computation of minimal absent words using suffix array Barton, Carl; Heliou, Alice; Mouchard, Laurent. - : BioMed Central, 2014 BASE Show details 19 Order-Preserving Suffix Trees and Their Algorithmic Applications ... Crochemore, Maxime; Iliopoulos, Costas S.; Kociumaka, Tomasz. - : arXiv, 2013 BASE Show details

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