Related papers: Cut-Down de Bruijn Sequences
We study algorithms for solving the problem of constructing a text (long string) from a dictionary (sequence of small strings). The problem has an application in bioinformatics and has a connection with the Sequence assembly method for…
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.…
Longest common extension queries (LCE queries) and runs are ubiquitous in algorithmic stringology. Linear-time algorithms computing runs and preprocessing for constant-time LCE queries have been known for over a decade. However, these…
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., recursive…
In the longest common substring (LCS) problem, we are given two strings $S$ and $T$, each of length at most $n$, and we are asked to find a longest string occurring as a fragment of both $S$ and $T$. This is a classical and well-studied…
A special type of cyclic sequences named adjacency-hopping de Bruijn sequences is introduced in this paper. It is theoretically proved the existence of such sequences, and the number of such sequences is derived. These sequences guarantee…
The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…
A seed in a word is a relaxed version of a period in which the occurrences of the repeating subword may overlap. We show a linear-time algorithm computing a linear-size representation of all the seeds of a word (the number of seeds might be…
In the deletion channel, an important problem is to determine the number of subsequences derived from a string $U$ of length $n$ when subjected to $t$ deletions. It is well-known that the number of subsequences in the setting exhibits a…
This paper introduces the de Bruijn graph edge minimization problem, which is related to the compression of de Bruijn graphs: find the order-k de Bruijn graph with minimum edge count among all orders. We describe an efficient algorithm that…
We present the first $\mathrm{o}(n)$-space polynomial-time algorithm for computing the length of a longest common subsequence. Given two strings of length $n$, the algorithm runs in $\mathrm{O}(n^{3})$ time with $\mathrm{O}\left(\frac{n…
Universal Cycles, or U-cycles, as originally defined by de Bruijn, are an efficient method to exhibit a large class of combinatorial objects in a compressed fashion, and with no repeats. de Bruijn's theorem states that U-cycles for $n$…
The deletion distance between two binary words $u,v \in \{0,1\}^n$ is the smallest $k$ such that $u$ and $v$ share a common subsequence of length $n-k$. A set $C$ of binary words of length $n$ is called a $k$-deletion code if every pair of…
The longest common subsequence (LCS) problem is a central problem in stringology that finds the longest common subsequence of given two strings $A$ and $B$. More recently, a set of four constrained LCS problems (called generalized…
The nodes of the de Bruijn graph B(d,3) consist of all strings of length 3, taken from an alphabet of size d, with edges between words which are distinct substrings of a word of length 4. We give an inductive characterization of the maximum…
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…
The current paper is a study in Recurrent Neural Networks (RNN), motivated by the lack of examples simple enough so that they can be thoroughly understood theoretically, but complex enough to be realistic. We constructed an example of…
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…
In the recent research of data mining, frequent structures in a sequence of graphs have been studied intensively, and one of the main concern is changing structures along a sequence of graphs that can capture dynamic properties of data. On…