Related papers: Extending de Bruijn sequences to larger alphabets
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
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…
This paper is focused in designing an efficient on-line algorithm to reconstruct a DNA sequence and search the genes in it, we assume that the segment have no mutation or reading error, the algorithm is based on de Bruijn Graph for…
We study the Kronecker symbol $\left(\frac st\right)$ for the sequence of the convergents $s/t$ of a purely periodic continued fraction expansion. Whereas the corresponding sequence of Jacobi symbols is always periodic, it turns out that…
A connected digraph in which the in-degree of any vertex equals its out-degree is Eulerian; this baseline result is used as the basis of existence proofs for universal cycles (also known as deBruijn cycles or $U$-cycles) of several…
We investigate the structure of graphs of twin-width at most $1$, and obtain the following results: - Graphs of twin-width at most $1$ are permutation graphs. In particular they have an intersection model and a linear structure. - There is…
Let L be an infinite regular language on a totally ordered alphabet (A,<). Feeding a finite deterministic automaton (with output) with the words of L enumerated lexicographically with respect to < leads to an infinite sequence over the…
In this paper we study pseudorandomness of a family of sequences in terms of two measures, the family complexity ($f$-complexity) and the cross-correlation measure of order $\ell$. We consider sequences not only on binary alphabet but also…
Genome assembly tools based on the de Bruijn graph framework rely on a parameter k, which represents a trade-off between several competing effects that are difficult to quantify. There is currently a lack of tools that would automatically…
A graph is $k$-clique-extendible if there is an ordering of the vertices such that whenever two $k$-sized overlapping cliques $A$ and $B$ have $k-1$ common vertices, and these common vertices appear between the two vertices $a,b\in…
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…
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 $O(n \log g)$…
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…
Finding all maximal $k$-plexes on networks is a fundamental research problem in graph analysis due to many important applications, such as community detection, biological graph analysis, and so on. A $k$-plex is a subgraph in which every…
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…
Finding the longest common subsequence in $k$-length substrings (LCS$k$) is a recently proposed problem motivated by computational biology. This is a generalization of the well-known LCS problem in which matching symbols from two sequences…
The generation of random graphs using edge swaps provides a reliable method to draw uniformly random samples of sets of graphs respecting some simple constraints, e.g. degree distributions. However, in general, it is not necessarily…
We consider the degree-diameter problem for undirected and directed circulant graphs. To date, attempts to generate families of large circulant graphs of arbitrary degree for a given diameter have concentrated mainly on the diameter 2 case.…
A $d$-subsequence of a sequence $\varphi = x_1\dots x_n$ is a subsequence $x_i x_{i+d} x_{i+2d} \dots$, for any positive integer $d$ and any $i$, $1 \le i \le n$. A \textit{$k$-Thue sequence} is a sequence in which every $d$-subsequence,…
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…