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- Florin Manea, Robert Mercas
- Theor. Comput. Sci.
- 2007

The paper approaches the classical combinatorial problem of free-ness of words, in the more general case of partial words. First, we propose an algorithm that tests efficiently whether a partial word is k-free or not. Then, we show that there exist arbitrarily many cube-free infinite partial words containing an infinite number of holes, over binary… (More)

Pseudo-repetitions are a natural generalization of the classical notion of repetitions in sequences. We solve fundamental algorithmic questions on pseudo-repetitions by application of insightful combinatorial results on words. More precisely, we efficiently decide whether a word is a pseudo-repetition and find all the pseudo-repetitive factors of a word. 1… (More)

- Francine Blanchet-Sadri, Robert Mercas, Geoffrey Scott
- Acta Cybern.
- 2008

A well known result of Fraenkel and Simpson states that the number of distinct squares in a word of length n is bounded by 2n since at each position there are at most two distinct squares whose last occurrence start. In this paper, we investigate the problem of counting distinct squares in partial words, or sequences over a finite alphabet that may have… (More)

Erdös raised the question whether there exist infinite abelian square-free words over a given alphabet (words in which no two adjacent subwords are permutations of each other). Infinite abelian square-free words have been constructed over alphabets of sizes as small as four. In this paper, we investigate the problem of avoiding abelian squares in partial… (More)

- Robert Mercas, Aleksi Saarela
- RAIRO - Theor. Inf. and Applic.
- 2013

A k-abelian cube is a word uvw, where u, v, w have the same factors of length at most k with the same multiplicities. Previously it has been known that k-abelian cubes are avoidable over a binary alphabet for k ≥ 5. Here it is proved that this holds for k ≥ 3.

We propose an algorithm that given as input a full word w of length n, and positive integers p and d, outputs (if any exists) a maximal p-periodic partial word contained in w with the property that no two holes are within distance d. Our algorithm runs in O(nd) time and is used for the study of freeness of partial words. Furthermore, we construct an… (More)

- Francine Blanchet-Sadri, Jane I. Kim, Robert Mercas, William Severa, Sean Simmons, Dimin Xu
- J. Comb. Theory, Ser. A
- 2012

Erdös raised the question whether there exist infinite abelian square-free words over a given alphabet, that is, words in which no two adjacent subwords are permutations of each other. It can easily be checked that no such word exists over a three-letter alphabet. However, infinite abelian square-free words have been constructed over alphabets of sizes as… (More)

- Roberto Grossi, Costas S. Iliopoulos, +4 authors Fatima Vayani
- Algorithms for Molecular Biology
- 2016

Sequence comparison is a fundamental step in many important tasks in bioinformatics; from phylogenetic reconstruction to the reconstruction of genomes. Traditional algorithms for measuring approximation in sequence comparison are based on the notions of distance or similarity, and are generally computed through sequence alignment techniques. As circular… (More)

- Francine Blanchet-Sadri, Robert Mercas, Sean Simmons, Eric Weissenstein
- Acta Informatica
- 2010

The problem of classifying all the avoidable binary patterns in (full) words has been completely solved (see Chap. 3 of M. Lothaire, Algebraic Combinatorics on Words, Cambridge University Press, 2002). In this paper, we classify all the avoidable binary patterns in partial words, or sequences that may have some undefined positions called holes. In… (More)

- Henning Fernau, Florin Manea, Robert Mercas, Markus L. Schmid
- STACS
- 2015

A pattern (i. e., a string of variables and terminals) maps to a word, if this is obtained by uniformly replacing the variables by terminal words; deciding this is N P-complete. We present efficient algorithms 1 that solve this problem for restricted classes of patterns. Furthermore, we show that it is N P-complete to decide, for a given number k and a word… (More)