Related papers: Extending de Bruijn sequences to larger alphabets

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…

This paper describes new, simple, recursive methods of construction for orientable sequences, i.e. periodic binary sequences in which any n-tuple occurs at most once in a period in either direction. As has been previously described, such…

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…

We use modular arithmetic to construct a de Bruijn array containing all fillings of an L (a 2 x 2 array with the upper right corner removed) with digits chosen from {0,...,k-1}.

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 propose a construction of de Bruijn sequences by the cycle joining method from linear feedback shift registers (LFSRs) with arbitrary characteristic polynomial $f(x)$. We study in detail the cycle structure of the set $\Omega(f(x))$ that…

We study a construction published by Donald Knuth in 1965 yielding a completely uniformly distributed sequence of real numbers. Knuth's work is based on de Bruijn sequences of increasing orders and alphabet sizes, which grow exponentially…

We introduce a new concept of a subgraph class called a superbubble for analyzing assembly graphs, and propose an efficient algorithm for detecting it. Most assembly algorithms utilize assembly graphs like the de Bruijn graph or the overlap…

Given an alphabet $S$, we consider the size of the subsets of the full sequence space $S^{\rm {\bf Z}}$ determined by the additional restriction that $x_i\not=x_{i+f(n)},\ i\in {\rm {\bf Z}},\ n\in {\rm {\bf N}}.$ Here $f$ is a positive,…

A balanced generalized de Bruijn sequence with parameters $(n,l,k)$ is a cyclic sequence of $n$ bits such that (a) the number of 0's equals the number of 1's, and (b) each substring of length $l$ occurs at most $k$ times. We determine…

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…

Motivated by the known autocorrelation properties of the Rudin-Shapiro sequence, we study the discrete correlation among infinite sequences over a finite alphabet, where we just take into account whether two symbols are identical. We show…

In this thesis, we address the problem of identifying and quantifying variants (alternative splicing and genomic polymorphism) in RNA-seq data when no reference genome is available, without assembling the full transcripts. Based on the…

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…

Let $X_1, X_2, ..., X_n, ... $ be a sequence of iid random variables with values in a finite alphabet $\{1,...,m\}$. Let $LI_n$ be the length of the longest increasing subsequence of $X_1, X_2, ..., X_n.$ We express the limiting…

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…

Time series clustering poses a significant challenge with diverse applications across domains. A prominent drawback of existing solutions lies in their limited interpretability, often confined to presenting users with centroids. In…

De Bruijn graph is one of the most important data structures used in de-novo genome assembly algorithms, especially for NGS data. There is a growing need for parallel data structures and algorithms due to the increasing number of cores in…

We develop a new approach to random walks on de Bruijn graphs over the alphabet $A$ through right congruences on $A^k$, defined using the natural right action of $A^+$. A major role is played by special right congruences, which correspond…

In this article, we show how to transform a colored de Bruijn graph (dBG) into a practical index for processing massive sets of sequencing reads. Similar to previous works, we encode an instance of a colored dBG of the set using BOSS and a…