Related papers: Generalized Orthogonal de Bruijn and Kautz Sequenc…

There are several approaches to study occurrences of consecutive patterns in permutations such as the inclusion-exclusion method, the tree representations of permutations, the spectral approach and others. We propose yet another approach to…

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…

The k-spectrum of a string is the set of all distinct substrings of length k occurring in the string. K-spectra have many applications in bioinformatics including pseudoalignment and genome assembly. The Spectral Burrows-Wheeler Transform…

Frequent sequence mining methods often make use of constraints to control which subsequences should be mined. A variety of such subsequence constraints has been studied in the literature, including length, gap, span, regular-expression, and…

What is the length of the shortest sequence $S$ of reals so that the set of consecutive $n$-words in $S$ form a covering code for permutations on $\{1,2, >..., n\}$ of radius $R$ ? (The distance between two $n$-words is the number of…

Finding the longest common subsequence in $k$-length substrings (LCS$k$) is a recently proposed problem motivated by computational biology. This is a generalization of the well-known LCS problem in which matching symbols from two sequences…

A simple graph G is k-ordered (respectively, k-ordered hamiltonian) if, for any sequence of k distinct vertices v_1, ..., v_k of G, there exists a cycle (respectively, a hamiltonian cycle) in G containing these k vertices in the specified…

Negative orientable sequences, i.e. periodic sequences with elements from a finite alphabet of size at least three in which an n-tuple or the negative of its reverse appears at most once in a period of the sequence, were introduced by…

de Bruijn sequences of order $\ell$, i.e., sequences that contain each $\ell$-tuple as a window exactly once, have found many diverse applications in information theory and most recently in DNA storage. This family of binary sequences has…

Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories -- based on the data structures which…

We study an interesting family of cooperating coroutines, which is able to generate all patterns of bits that satisfy certain fairly general ordering constraints, changing only one bit at a time. (More precisely, the directed graph of…

A Barker sequence is a binary sequence for which all nontrivial aperiodic autocorrelations are at most 1 in magnitude. An old conjecture due to Turyn asserts that there is no Barker sequence of length greater than 13. In 1961, Turyn and…

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…

We introduce the Parikh-de-Bruijn grid, a graph whose vertices are fixed-order Parikh vectors, and whose edges are given by a simple shift operation. This graph gives structural insight into the nature of sets of Parikh vectors as well as…

Cutwidth is one of the classic layout parameters for graphs. It measures how well one can order the vertices of a graph in a linear manner, so that the maximum number of edges between any prefix and its complement suffix is minimized. As…

Universal cycles are generalizations of de Bruijn cycles and Gray codes that were introduced originally by Chung, Diaconis, and Graham in 1990. They have been developed by many authors since, for various combinatorial objects such as…

The equidistant subsequence pattern matching problem is considered. Given a pattern string $P$ and a text string $T$, we say that $P$ is an \emph{equidistant subsequence} of $T$ if $P$ is a subsequence of the text such that consecutive…

Despite strong performance on a variety of tasks, neural sequence models trained with maximum likelihood have been shown to exhibit issues such as length bias and degenerate repetition. We study the related issue of receiving…

A $k$-mismatch square is a string of the form $XY$ where $X$ and $Y$ are two equal-length strings that have at most $k$ mismatches. Kolpakov and Kucherov [Theor. Comput. Sci., 2003] defined two notions of $k$-mismatch repeats, called…

We put forward new general criteria to design successor rules that generate binary de Bruijn sequences. Prior fast algorithms based on successor rules in the literature are then shown to be special instances. We implemented the criteria to…