Related papers: Arbitrary-length analogs to de Bruijn sequences
The algorithmic tasks of computing the Hamming distance between a given pattern of length $m$ and each location in a text of length $n$ is one of the most fundamental algorithmic tasks in string algorithms. Unfortunately, there is evidence…
We present the first linear time algorithm to construct the $2n$-bit version of the Lyndon array for a string of length $n$ using only $o(n)$ bits of working space. A simpler variant of this algorithm computes the plain ($n\lg n$-bit)…
Let $S$ be a string of length $n$ over an alphabet $\Sigma$ and let $Q$ be a subset of $\Sigma$ of size $q \geq 2$. The 'co-occurrence problem' is to construct a compact data structure that supports the following query: given an integer $w$…
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…
A sequence $S=s_{1}s_{2}..._{n}$ is \emph{nonrepetitive} if no two adjacent blocks of $S$ are identical. In 1906 Thue proved that there exist arbitrarily long nonrepetitive sequences over 3-element set of symbols. We study a generalization…
A Lyndon word is a primitive string which is lexicographically smallest among cyclic permutations of its characters. Lyndon words are used for constructing bases in free Lie algebras, constructing de Bruijn sequences, finding the…
The focus of this work is to show how to combine Zech's logarithms and each of the cycle joining and cross-join pairing methods to construct binary de Bruijn sequences of any order. A basic implementation is supplied as a proof-of-concept.…
This paper initiates the study of shortening universal cycles (u-cycles) and universal words (u-words) for permutations either by using incomparable elements, or by using non-deterministic symbols. The latter approach is similar in nature…
Non-linear recurrences which generate integers in a surprising way have been studied by many people. Typically people study recurrences that are linear in the highest order term. In this paper I consider what happens when the recurrence is…
The set of permutations on a finite set can be given the lattice structure known as the weak Bruhat order. This lattice structure is generalized to the set of words on a fixed alphabet $\Sigma$ = {x,y,z,...}, where each letter has a fixed…
Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories -- based on the data structures which…
The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…
The linear complexity of a sequence $s$ is one of the measures of its predictability. It represents the smallest degree of a linear recursion which the sequence satisfies. There are several algorithms to find the linear complexity of a…
Random residue sequences (RR) may be used in many random number applications including those related to multiple access in communications. This paper investigates variations on an algorithm to generate RR sequences that was proposed earlier…
Enumerating the number of times one word occurs in another is a much-studied combinatorial subject. By utilizing a method that we call ``lexicographic extreme referencing'', we provide a formula for computing occurrences of one binary word…
The fundamental question considered in algorithms on strings is that of indexing, that is, preprocessing a given string for specific queries. By now we have a number of efficient solutions for this problem when the queries ask for an exact…
Unlabelled Necklaces are an equivalence class of cyclic words under both the rotation (cyclic shift) and the relabelling operations. The relabelling of a word is a bijective mapping from the alphabet to itself. The main result of the paper…
This paper investigates the number of quantum queries made to solve the problem of reconstructing an unknown string from its substrings in a certain query model. More concretely, the goal of the problem is to identify an unknown string $S$…
Let H be a countable subgroup of the metrizable compact abelian group G and f:H -> T=R/Z a (not necessarily continuous) character of H. Then there exists a sequence (chi_n)_n of (continuous) characters of G such that lim_n chi_n(alpha) =…
We construct examples of Delone sets of the plane (that is, discrete subsets that are uniformly separated and coarsely dense) that are repetitive (each patch of the set appears in every large-enough ball) though non-rectifiable (i.e. non…