Related papers: Generalized Orthogonal de Bruijn and Kautz Sequenc…
Aligning a sequence to a walk in a labeled graph is a problem of fundamental importance to Computational Biology. For finding a walk in an arbitrary graph with $|E|$ edges that exactly matches a pattern of length $m$, a lower bound based on…
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…
The focus of this work is to show how to combine Zech's logarithms and each of the cycle joining and cross-join pairing methods to construct binary de Bruijn sequences of any order. A basic implementation is supplied as a proof-of-concept.…
De novo DNA assembly is a fundamental task in Bioinformatics, and finding Eulerian paths on de Bruijn graphs is one of the dominant approaches to it. In most of the cases, there may be no one order for the de Bruijn graph that works well…
Universal cycles are generalizations of de Bruijn cycles and Gray codes that were introduced originally by Chung, Diaconis, and Graham in 1992. They have been developed by many authors since, for various combinatorial objects such as…
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…
Negative avoiding sequences of span $n$ are periodic sequences of elements from $\mathbb{Z}_k$ for some $k$ with the property that no $n$-tuple occurs more than once in a period and if an $n$-tuple does occur then its negative does not.…
For a set of integers $I$, we define a $q$-ary $I$-cycle to be a assignment of the symbols 1 through $q$ to the integers modulo $q^n$ so that every word appears on some translate of $I$. This definition generalizes that of de Bruijn cycles,…
We define generalized de Bruijn words as those words having a Burrows-Wheeler transform that is a concatenation of permutations of the alphabet. We show that generalized de Bruijn words are in 1-to-1 correspondence with Hamiltonian cycles…
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.…
Universal cycles, such as De Bruijn cycles, are cyclic sequences of symbols that represent every combinatorial object from some family exactly once as a consecutive subsequence. Graph universal cycles are a graph analogue of universal…
De Bruijn tori, or perfect maps, are two-dimensional periodic arrays of letters from a finite alphabet, where each possible pattern of shape (m,n) appears exactly once in a single period. While the existence of certain de Bruijn tori, such…
Aperiodic autocorrelation is an important indicator of performance of sequences used in communications, remote sensing, and scientific instrumentation. Knowing a sequence's autocorrelation function, which reports the autocorrelation at…
We show that for every $n \geq 1$ and over any finite alphabet, there is a word whose circular factors of length $n$ have a one-to-one correspondence with the set of primitive words. In particular, we prove that such a word can be obtained…
We introduce and investigate binary $(k,k)$-designs -- combinatorial structures which are related to binary orthogonal arrays. We derive general linear programming bound and propose as a consequence a universal bound on the minimum possible…
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 sequence a_1,...,a_m is a common subsequence in the set of permutations S = {p_1,...,p_k} on [n] if it is a subsequence of p_i(1),...,p_i(n) and p_j(1),...,p_j(n) for some distinct p_i, p_j in S. Recently, Beame and Huynh-Ngoc (2008)…
This paper initiates the study of shortening universal cycles (u-cycles) and universal words (u-words) for permutations either by using incomparable elements, or by using non-deterministic symbols. The latter approach is similar in nature…
The de Bruijn torus (or grid) problem looks to find an $n$-by-$m$ binary matrix in which every possible $j$-by-$k$ submatrix appears exactly once. The existence and construction of these binary matrices was determined in the 70's, with…
We study universal compression of sequences generated by monotonic distributions. We show that for a monotonic distribution over an alphabet of size $k$, each probability parameter costs essentially $0.5 \log (n/k^3)$ bits, where $n$ is the…