Related papers: Efficient constructions of the Prefer-same and Pre…

We propose a general greedy algorithm for binary de Bruijn sequences, called Generalized Prefer-Opposite (GPO) Algorithm, and its modifications. By identifying specific feedback functions and initial states, we demonstrate that most…

The well known prefer-one, prefer-opposite, and prefer-same binary de Bruijn sequences are all constructed using simple preference rules. We apply the technique of preference functions of span one to define q-ary sequences that generalize…

A shift rule for the prefer-max De Bruijn sequence is formulated, for all sequence orders, and over any finite alphabet. An efficient algorithm for this shift rule is presented, which has linear (in the sequence order) time and memory…

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…

Experimental results show that, when the order $n$ is odd, there are de Bruijn sequences such that the corresponding complement sequence and the reverse sequence are the same. In this paper, we propose one efficient method to generate such…

A cut-down de Bruijn sequence is a cyclic string of length $L$, where $1 \leq L \leq k^n$, such that every substring of length $n$ appears at most once. Etzion [Theor. Comp. Sci 44 (1986)] gives an algorithm to construct binary cut-down de…

We propose a novel construction for the well-known prefer-max De Bruijn sequence, based on the cycle joining technique. We further show that the construction implies known results from the literature in a straightforward manner. First, it…

The de Bruijn graph $G_K$ of a set of strings $S$ is a key data structure in genome assembly that represents overlaps between all the $K$-length substrings of $S$. Construction and navigation of the graph is a space and time bottleneck in…

Recently, Marcus et al. (Bioinformatics 2014) proposed to use a compressed de Bruijn graph to describe the relationship between the genomes of many individuals/strains of the same or closely related species. They devised an $O(n \log g)$…

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…

The design of uniformly spread sequences on $[0,1)$ has been extensively studied since the work of Weyl and van der Corput in the early $20^{\text{th}}$ century. The current best sequences are based on the Kronecker sequence with golden…

One of the fundamental ways to construct De Bruijn sequences is by using a shift-rule. A shift-rule receives a word as an argument and computes the symbol that appears after it in the sequence. An optimal shift-rule for an $(n,k)$-De Bruijn…

We study a fixed-window counting system in which integers are represented by words of constant length while the alphabet grows as needed. This viewpoint arises from De Bruijn sequences: for fixed order $n$, the reverse prefer-max sequence…

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., recursive…

The de Bruijn graph, its sequences, and their various generalizations, have found many applications in information theory, including many new ones in the last decade. In this paper, motivated by a coding problem for emerging memory…

Orientable sequences of order n are infinite periodic sequences with symbols drawn from a finite alphabet of size k with the property that any particular subsequence of length n occurs at most once in a period in either direction. They were…

We present the first linear time algorithm to construct the $2n$-bit version of the Lyndon array for a string of length $n$ using only $o(n)$ bits of working space. A simpler variant of this algorithm computes the plain ($n\lg n$-bit)…

A nonbinary Ford sequence is a de Bruijn sequence generated by simple rules that determine the priorities of what symbols are to be tried first, given an initial word of size $n$ which is the order of the sequence being generated. This set…

Collective communications are ubiquitous in parallel applications. We present two new algorithms for performing a reduction. The operation associated with our reduction needs to be associative and commutative. The two algorithms are…

A de Bruijn sequence of order $k$ over a finite alphabet is a cyclic sequence with the property that it contains every possible $k$-sequence as a substring exactly once. Orthogonal de Bruijn sequences are collections of de Bruijn sequences…