Related papers: Extending de Bruijn sequences to larger alphabets

The linear complexity and k-error linear complexity of a sequence have been used as important measures of keystream strength, hence designing a sequence with high linear complexity and $k$-error linear complexity is a popular research topic…

Massively parallel DNA sequencing technologies are revolutionizing genomics research. Billions of short reads generated at low costs can be assembled for reconstructing the whole genomes. Unfortunately, the large memory footprint of the…

A graph $G=(V,E)$ is word-representable if there exists a word $w$ over the alphabet $V$ such that letters $x$ and $y$ alternate in $w$ if and only if $xy\in E$. Word-representable graphs generalize several important classes of graphs such…

The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we…

We present practical algorithms for generating universal cycles uniformly at random. In particular, we consider universal cycles for shorthand permutations, subsets and multiset permutations, weak orders, and orientable sequences.…

We show that a 1969 result of Bouwkamp and de Bruijn on a formal power series expansion can be interpreted as the hypergraph analogue of the fact that every connected graph with n vertices has at least n-1 edges. We explain some of Bouwkamp…

Intrinsic Diophantine approximation on fractals, such as the Cantor ternary set, was undoubtedly motivated by questions asked by K. Mahler (1984). One of the main goals of this paper is to develop and utilize the theory of infinite de…

The first step in any genome assembly algorithm entails the conversion from the domain of strings and overlaps to the language of graphs and paths, typically using one of the two conventional methods: de Bruijn graphs or overlap graphs.…

Let us call a sequence of numbers heapable if they can be sequentially inserted to form a binary tree with the heap property, where each insertion subsequent to the first occurs at a leaf of the tree, i.e. below a previously placed number.…

Analogously to de Bruijn sequences, orientable sequences have application in automatic position-location applications and, until recently, studies of these sequences focused on the binary case. In recent work by Alhakim et al., a range of…

Fix a finite alphabet. A necklace is a circular word. For positive integers $n$ and~$k$, a necklace is $(n,k)$-perfect if all words of length $n$ occur $k$ times but at positions with different congruence modulo $k$, for any convention of…

We study how to generate binary de Bruijn sequences efficiently from the class of simple linear feedback shift registers with feedback function $f(x_0, x_1, \ldots, x_{n-1}) = x_0 + x_1 + x_{n-1}$ for $n \geq 3$, using the cycle joining…

Using greedy algorithms to generate de Bruijn sequences is a classical approach that has produced numerous interesting theoretical results. This paper investigates an algorithm which we call the Generalized Prefer-Opposite (GPO). It…

The discrepancy of a binary string refers to the maximum (absolute) difference between the number of ones and the number of zeroes over all possible substrings of the given binary string. We provide an investigation of the discrepancy of…

A constructive method is provided that outputs a directed graph which is named a broken crown graph, containing $5n-9$ vertices and $k$ Hamiltonian cycles for any choice of integers $n \geq k \geq 4$. The construction is not designed to be…

We present a method which displays all palindromes of a given length from De Bruijn words of a certain order, and also a recursive one which constructs all palindromes of length $n+1$ from the set of palindromes of length $n$. We show that…

An M-sequence generated by a primitive polynomial has many interesting and desirable properties. A pseudo-random array is the two-dimensional generalization of an M-sequence. There are non-primitive polynomials all of whose non-zero…

We prove a lower bound on the length of the longest $j$-tight cycle in a $k$-uniform binomial random hypergraph for any $2 \le j \le k-1$. We first prove the existence of a $j$-tight path of the required length. The standard "sprinkling"…

The skew of a binary string is the difference between the number of zeroes and the number of ones, while the length of the string is the sum of these two numbers. We consider certain suffixes of the lexicographically-least de Bruijn…

The reduction of the fragment assembly problem to (variations of) the classical Eulerian trail problem [Pevzner et al., PNAS 2001] has led to remarkable progress in genome assembly. This reduction employs the notion of de Bruijn graph…