Related papers: Algorithmical Aspects of Some Bio Inspired Operati…
An infinite permutation $\alpha$ is a linear ordering of $\mathbb N$. We study properties of infinite permutations analogous to those of infinite words, and show some resemblances and some differences between permutations and words. In this…
We revisit the topic of power-free morphisms, focusing on the properties of the class of complementary morphisms. Such morphisms are defined over a $2$-letter alphabet, and map the letters 0 and 1 to complementary words. We prove that every…
We study the fundamental question of how efficiently suffix array entries can be accessed when the array cannot be stored explicitly. The suffix array $SA_T[1..n]$ of a text $T$ of length $n$ encodes the lexicographic order of its suffixes…
We study word structures of the form $(D,<,P)$ where $D$ is either $\mathbb{N}$ or $\mathbb{Z}$, $<$ is the natural linear ordering on $D$ and $P\subseteq D$ is a predicate on $D$. In particular we show: (a) The set of recursive…
Gene duplication is a fundamental evolutionary mechanism that contributes to biological complexity and diversity (Fortna et al., 2004). Traditionally, research has focused on the duplication of gene sequences (Zhang, 1914). However,…
Letting $w$ denote a finite, nonempty word, let $\text{red}(w)$ denote the word obtained from $w$ by replacing every subword $s$ of $w$ of the form $cc \cdots c$ for a given character $c$ (such that there is no character immediately to the…
We study infinite words fixed by a morphism and their derived words. A derived word is a coding of return words to a factor. We exhibit two examples of sets of morphisms which are closed under derivation --- any derived word with respect to…
In this paper we introduce and study new notions of uniform recurrence in multidimensional words. A $d$-dimensional word is called \emph{uniformly recurrent} if for all $(s_1,\ldots,s_d)\in\mathbb{N}^d$ there exists $n\in\mathbb{N}$ such…
The hairpin completion is an operation on formal languages that has been inspired by the hairpin formation in DNA biochemistry and by DNA computing. In this paper we investigate the hairpin completion of regular languages. It is well known…
We study various aspects of Dyck words appearing in binary sequences, where $0$ is treated as a left parenthesis and $1$ as a right parenthesis. We show that binary words that are $7/3$-power-free have bounded nesting level, but this no…
We study the duplication with transposition distance between strings of length $n$ over a $q$-ary alphabet and their roots. In other words, we investigate the number of duplication operations of the form $x = (abcd) \to y = (abcbd)$, where…
Two strings $x$ and $y$ over $\Sigma \cup \Pi$ of equal length are said to \emph{parameterized match} (\emph{p-match}) if there is a renaming bijection $f:\Sigma \cup \Pi \rightarrow \Sigma \cup \Pi$ that is identity on $\Sigma$ and…
Many different deletion operations are investigated applied to languages accepted by one-way and two-way deterministic reversal-bounded multicounter machines, deterministic pushdown automata, and finite automata. Operations studied include…
We study the complexity of basic regular operations on languages represented by incomplete deterministic or nondeterministic automata, in which all states are final. Such languages are known to be prefix-closed. We get tight bounds on both…
In computational biology, tandem duplication is an important biological phenomenon which can occur either at the genome or at the DNA level. A tandem duplication takes a copy of a genome segment and inserts it right after the segment - this…
We examine deterministic and nondeterministic state complexities of regular operations on prefix-free languages. We strengthen several results by providing witness languages over smaller alphabets, usually as small as possible. We next…
A bidimensional bifix (in short bibifix) of a square matrix T is a square submatrix of T which occurs in the top-left and bottom-right corners of T. This allows us to extend the definition of bifix-free words and cross-bifix-free set of…
Two words are $k$-binomially equivalent if each subword of length at most $k$ occurs the same number of times in both words. The $k$-binomial complexity of an infinite word is a counting function that maps $n$ to the number of $k$-binomial…
Two words are $k$-binomially equivalent whenever they share the same subwords, i.e., subsequences, of length at most $k$ with the same multiplicities. This is a refinement of both abelian equivalence and the Simon congruence. The…
Motivated by DNA storage in living organisms, and by known biological mutation processes, we study the reverse-complement string-duplication system. We fully classify the conditions under which the system has full expressiveness, for all…