Related papers: Algorithmical Aspects of Some Bio Inspired Operati…
Hairpin completion and its variant called bounded hairpin completion are operations on formal languages, inspired by a hairpin formation in molecular biology. Another variant called hairpin lengthening has been recently introduced and…
We present a new recursive generation algorithm for prefix normal words. These are binary strings with the property that no substring has more 1s than the prefix of the same length. The new algorithm uses two operations on binary strings,…
Iterated hairpin completion is an operation on formal languages that is inspired by the hairpin formation in DNA biochemistry. Iterated hairpin completion of a word (or more precisely a singleton language) is always a context-sensitive…
Tandem duplication is an evolutionary process whereby a segment of DNA is replicated and proximally inserted. The different configurations that can arise from this process give rise to some interesting combinatorial questions. Firstly, we…
The (bounded) hairpin completion and its iterated versions are operations on formal lan- guages which have been inspired by the hairpin formation in DNA-biochemistry. The paper answers two questions asked in the literature about the…
Following Inoue et al., we define a word to be a repetition if it is a (fractional) power of exponent at least 2. A word has a repetition factorization if it is the product of repetitions. We study repetition factorizations in several…
This paper presents a constraint-based morphological disambiguation approach that is applicable languages with complex morphology--specifically agglutinative languages with productive inflectional and derivational morphological phenomena.…
Repetition avoidance has been studied since Thue's work. In this paper, we considered another type of repetition, which is called pseudo-power. This concept is inspired by Watson-Crick complementarity in DNA sequence and is defined over an…
Given a countable set X (usually taken to be the natural numbers or integers), an infinite permutation, \pi, of X is a linear ordering of X. This paper investigates the combinatorial complexity of infinite permutations on the natural…
Given a countable set X (usually taken to be N or Z), an infinite permutation $\pi$ of X is a linear ordering $<_\pi$ of X. This paper investigates the combinatorial complexity of infinite permutations on N associated with the image of…
Hairpin completion is an abstract operation modeling a DNA bio-operation which receives as input a DNA strand $w = x\alpha y \calpha$, and outputs $w' = x \alpha y \bar{\alpha} \bar{x}$, where $\bar{x}$ denotes the Watson-Crick complement…
A prefix normal word is a binary word with the property that no substring has more 1s than the prefix of the same length. This class of words is important in the context of binary jumbled pattern matching. In this paper we present an…
Motivated by work on bio-operations on DNA strings, we consider an outfix-guided insertion operation that can be viewed as a generalization of the overlap assembly operation on strings studied previously. As the main result we construct a…
Prefix-free parsing (PFP) was introduced by Boucher et al. (2019) as a preprocessing step to ease the computation of Burrows-Wheeler Transforms (BWTs) of genomic databases. Given a string $S$, it produces a dictionary $D$ and a parse $P$ of…
A narrow connection between infinite binary words rich in classical palindromes and infinite binary words rich simultaneously in palindromes and pseudopalindromes (the so-called $H$-rich words) is demonstrated. The correspondence between…
We study a binary Thue--Morse-type sequence arising from the base-$3/2$ expansion of integers, an archetypal automatic sequence in a rational base numeration system. Because the sequence is generated by a periodic iteration of morphisms…
In the present paper we consider biologically motivated reduction operations on double occurrence words. Then we define the nesting index of a double occurrence word to be the least number of reduction operations it takes for a word to be…
A double occurrence word $w$ over a finite alphabet $\Sigma$ is a word in which each alphabet letter appears exactly twice. Such words arise naturally in the study of topology, graph theory, and combinatorics. Recently, double occurrence…
A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…
A \emph{morphism} is a mapping that transforms words through letter-wise substitution, where each symbol is consistently replaced by a fixed word. In the field of combinatorics on words, one topic that has attracted considerable attention…