Related papers: Arbitrary-length analogs to de Bruijn sequences

Suppose we want to seek the longest common subsequences (LCSs) of two strings as informative patterns that explain the relationship between the strings. The dynamic programming algorithm gives us a table from which all LCSs can be extracted…

Given a string $T$ with length $n$ whose characters are drawn from an ordered alphabet of size $\sigma$, its longest Lyndon subsequence is a longest subsequence of $T$ that is a Lyndon word. We propose algorithms for finding such a…

A {\it superpattern} is a string of characters of length $n$ that contains as a subsequence, and in a sense that depends on the context, all the smaller strings of length $k$ in a certain class. We prove structural and probabilistic results…

We present a new recursive generation algorithm for prefix normal words. These are binary strings with the property that no substring has more 1s than the prefix of the same length. The new algorithm uses two operations on binary strings,…

Various specifiable combinatorial structures, with d extensive parameters, can be exactly sampled both by the recursive method, with linear arithmetic complexity if a heavy preprocessing is performed, or by the Boltzmann method, with…

We determine the average number of distinct subsequences in a random binary string, and derive an estimate for the average number of distinct subsequences of a particular length.

It is a classical fact that for any $\varepsilon > 0$, a random permutation of length $n = (1 + \varepsilon) k^2 / 4$ typically contains a monotone subsequence of length $k$. As a far-reaching generalization, Alon conjectured that a random…

After defining a notion of $\epsilon$-density, we provide for any real algebraic number $\alpha$ an estimate of the smallest $\epsilon$ such that for each $m>1$ the set of vectors of the form $(t,t\alpha,...,t\alpha^{m-1})$ for $t\in\R$ is…

We analyse the number of occurrences of a fixed non-zero digit in the width-w non-adjacent forms of all elements of a lattice in some region (e.g. a ball). Our result is an asymptotic formula, where its main term coincides with the full…

Consider two independent random strings having same length and taking values uniformly in a common finite alphabet. We study the order of the variance of the length of the longest common subsequences (LCS) of these strings when long blocks,…

We consider the problem of binary string reconstruction from the multiset of its substring compositions, i.e., referred to as the substring composition multiset, first introduced and studied by Acharya et al. We introduce a new algorithm…

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…

This paper describes the probabilistic behaviour of a random Sturmian word. It performs the probabilistic analysis of the recurrence function which can be viewed as a waiting time to discover all the factors of length $n$ of the Sturmian…

Let $s$ be a finite sequence over a field of length $n$. It is well-known that if $s$ satisfies a linear recurrence of order $d$ with non-zero constant term, then the reverse of $s$ also satisfies a recurrence of order $d$ (with…

Let $\textbf{T}(n,k)$ be the set of strings of length $n$ over the alphabet $\Sigma=\{1,2,\ldots,k\}$. A universal cycle for $\textbf{T}(n,k)$ can be constructed using a greedy algorithm: start with the string $k^n$, and continually append…

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…

We say a string has a cadence if a certain character is repeated at regular intervals, possibly with intervening occurrences of that character. We call the cadence anchored if the first interval must be the same length as the others. We…

We consider the problem of identifying tandem scattered subsequences within a string. Our algorithm identifies a longest subsequence which occurs twice without overlap in a string. This algorithm is based on the Hunt-Szymanski algorithm,…

An $(m,n,R)$-de Bruijn covering array (dBCA) is a doubly periodic $M \times N$ array over an alphabet of size $q$ such that the set of all its $m \times n$ windows form a covering code with radius $R$. An upper bound of the smallest array…

Completely antipersistent binary time series are sequences in which every time that an $N$-bit string $\mu$ appears, the sequence is continued with a different bit than at the last occurrence of $\mu$. This dynamics is phrased in terms of a…