Related papers: Cut-Down de Bruijn Sequences
We propose a new camera-based method of robot identification, tracking and orientation estimation. The system utilises coloured lights mounted in a circle around each robot to create unique colour sequences that are observed by a camera.…
In the classic Minimum Bisection problem we are given as input a graph $G$ and an integer $k$. The task is to determine whether there is a partition of $V(G)$ into two parts $A$ and $B$ such that $||A|-|B|| \leq 1$ and there are at most $k$…
An $n$-length binary word is $q$-decreasing, $q\geq 1$, if every of its length maximal factor of the form $0^a1^b$ satisfies $a=0$ or $q\cdot a > b$.We show constructively that these words are in bijection with binary words having no…
The linear complexity of a sequence has been used as an important measure of keystream strength, hence designing a sequence which possesses high linear complexity and $k$-error linear complexity is a hot topic in cryptography and…
Sequence assembly from short reads is an important problem in biology. It is known that solving the sequence assembly problem exactly on a bi-directed de Bruijn graph or a string graph is intractable. However finding a Shortest Double…
We introduce the notion of unavoidable (complete) sets of word patterns, which is a refinement for that of words, and study certain numerical characteristics for unavoidable sets of patterns. In some cases we employ the graph of pattern…
Let w be a binary string and let a_w (n) be the number of occurrences of the word w in the binary expansion of n. As usual we let s(n) denote the Stern sequence; that is, s(0)=0, s(1)=1, and for n >= 1, s(2n)=s(n) and s(2n+1)=s(n)+s(n+1).…
de Bruijn graph-based algorithms are one of the two most widely used approaches for de novo genome assembly. A major limitation of this approach is the large computational memory space requirement to construct the de Bruijn graph, which…
We consider the problem of constructing binary codes to recover from $k$-bit deletions with efficient encoding/decoding, for a fixed $k$. The single deletion case is well understood, with the Varshamov-Tenengolts-Levenshtein code from 1965…
Recently, Conte et al. generalized the longest-common prefix (LCP) array from strings to Wheeler DFAs, and they showed that it can be used to efficiently determine matching statistics on a Wheeler DFA [DCC 2023]. However, storing the LCP…
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…
We describe new, simple, recursive methods of construction for orientable sequences over an arbitrary finite alphabet, i.e. periodic sequences in which any sub-sequence of n consecutive elements occurs at most once in a period in either…
The sequence reconstruction problem, introduced by Levenshtein in 2001, considers a communication scenario where the sender transmits a codeword from some codebook and the receiver obtains multiple noisy reads of the codeword. The common…
The sequence reconstruction problem was proposed by Levenshtein in 2001. In this model, a sequence from a code is transmitted over several channels, and the decoder receives the distinct outputs from each channel. The main problem is to…
In the Shortest-Superstring problem, we are given a set of strings S and want to find a string that contains all strings in S as substrings and has minimum length. This is a classical problem in approximation and the best known…
Longest common extension queries (often called longest common prefix queries) constitute a fundamental building block in multiple string algorithms, for example computing runs and approximate pattern matching. We show that a sequence of $q$…
A new method for constructing minimum-redundancy binary prefix codes is described. Our method does not explicitly build a Huffman tree; instead it uses a property of optimal prefix codes to compute the codeword lengths corresponding to the…
This paper proves the existence of $t$-identifying codes on the class of undirected de Bruijn graphs with string length $n$ and alphabet size $d$, referred to as $\mathcal{B}(d,n)$. It is shown that $\mathcal{B}(d,n)$ is $t$-identifiable…
A T-net of order $m$ is a graph with $m$ nodes and $2m$ directed edges, where every node has indegree and outdegree equal to $2$. (A well known example of T-nets are de Bruijn graphs.) Given a T-net $N$ of order $m$, there is the so called…
In this paper we address the constrained longest common subsequence problem. Given two sequences $X$, $Y$ and a constrained sequence $P$, a sequence $Z$ is a constrained longest common subsequence for $X$ and $Y$ with respect to $P$ if $Z$…