Related papers: The complexity of string partitioning

The problem of matching a query string to a directed graph, whose vertices are labeled by strings, has application in different fields, from data mining to computational biology. Several variants of the problem have been considered,…

Given strings $P$ of length $m$ and $T$ of length $n$ over an alphabet of size $\sigma$, the string matching with $k$-mismatches problem is to find the positions of all the substrings in $T$ that are at Hamming distance at most $k$ from…

In combinatorics on words, a word $w$ over an alphabet $\Sigma$ is said to avoid a pattern $p$ over an alphabet $\Delta$ if there is no factor $f$ of $w$ such that $f= (p)$ where $h: \Delta^*\to\Sigma^*$ is a non-erasing morphism. A pattern…

A set X of partial words over a finite alphabet A is called unavoidable if every two-sided infinite word over A has a factor compatible with an element of X. Unlike the case of a set of words without holes, the problem of deciding whether…

This is a review of a set of recent papers with some new data added. After a brief biological introduction a visualization scheme of the string composition of long DNA sequences, in particular, of bacterial complete genomes, will be…

It was suggested in hep-th/0002106, that semiclassically, a partition function of a string theory in the 5 dimensional constant negative curvature space with a boundary condition at the absolute satisfy the loop equation with respect to…

We examine the statistical properties of defects formed by the breaking of a U(1) symmetry when the Higgs field has a power spectrum $P(k) \propto k^n$. We find a marked dependence of the amount of infinite string on the spectral index $n$…

A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…

We discuss the obstacles for defining a set of observable quantities analogous to an S-matrix which are needed to formulate string theory in an accelerating universe. We show that the quintessence models with the equations of state $-1 < w…

The problem we consider is the following: Given an infinite word $w$ on an ordered alphabet, construct the sequence $\nu_w=(\nu[n])_n$, equidistributed on $[0,1]$ and such that $\nu[m]<\nu[n]$ if and only if $\sigma^m(w)<\sigma^n(w)$, where…

Let $P$ be a set of $m$ points in ${\mathbb R}^2$, let $\Sigma$ be a set of $n$ semi-algebraic sets of constant complexity in ${\mathbb R}^2$, let $(S,+)$ be a semigroup, and let $w: P \rightarrow S$ be a weight function on the points of…

We study algorithms for solving three problems on strings. The first one is the Most Frequently String Search Problem. The problem is the following. Assume that we have a sequence of $n$ strings of length $k$. The problem is finding the…

In this paper, we consider two versions of the Text Assembling problem. We are given a sequence of strings $s^1,\dots,s^n$ of total length $L$ that is a dictionary, and a string $t$ of length $m$ that is texts. The first version of the…

Given a sequence composed of a limit number of characters, we try to "read" it as a "text". This involves to segment the sequence into "words". The difficulty is to distinguish good segmentation from enormous number of random ones.Aiming at…

In this paper, we consider the satisfiability problem for string logic with equations, regular membership and Presburger constraints over length functions. The difficulty comes from multiple occurrences of string variables making…

The rank and select operations over a string of length n from an alphabet of size $\sigma$ have been used widely in the design of succinct data structures. In many applications, the string itself need be maintained dynamically, allowing…

We generalise a multiple string pattern matching algorithm, recently proposed by Fredriksson and Grabowski [J. Discr. Alg. 7, 2009], to deal with arbitrary dictionaries on an alphabet of size $s$. If $r_m$ is the number of words of length…

Exact string matching has been a fundamental problem in computer science for decades because of many practical applications. Some are related to common procedures, such as searching in files and text editors, or, more recently, to more…

String barcoding is a recently introduced technique for genomic-based identification of microorganisms. In this paper we describe the engineering of highly scalable algorithms for robust string barcoding. Our methods enable distinguisher…

The complexity function of an infinite word $w$ on a finite alphabet $A$ is the sequence counting, for each non-negative $n$, the number of words of length $n$ on the alphabet $A$ that are factors of the infinite word $w$. The goal of this…