Related papers: String 2-Covers with No Length Restrictions
An elastic-degenerate string is a sequence of $n$ finite sets of strings of total length $N$, introduced to represent a set of related DNA sequences, also known as a pangenome. The ED string matching (EDSM) problem consists in reporting all…
We introduce a novel definition of approximate palindromes in strings, and provide an algorithm to find all maximal approximate palindromes in a string with up to $k$ errors. Our definition is based on the usual edit operations of…
In the Maximum Duo-Preservation String Mapping problem we are given two strings and wish to map the letters of the former to the letters of the latter so as to maximise the number of duos. A duo is a pair of consecutive letters that is…
Regularities in strings are often related to periods and covers, which have extensively been studied, and algorithms for their efficient computation have broad application. In this paper we concentrate on computing cyclic regularities of…
The Longest Common Subsequence (LCS) is the problem of finding a subsequence among a set of strings that has two properties of being common to all and is the longest. The LCS has applications in computational biology and text editing, among…
Given a set of $k$ strings $I$, their longest common subsequence (LCS) is the string with the maximum length that is a subset of all the strings in $I$. A data-structure for this problem preprocesses $I$ into a data-structure such that the…
In this paper we present algorithms for several string problems in the Congested Clique model. In the Congested Clique model, $n$ nodes (computers) are used to solve some problem. The input to the problem is distributed among the nodes, and…
We develop a polynomial time $\Omega\left ( \frac 1R \log R \right)$ approximate algorithm for Max 2CSP-$R$, the problem where we are given a collection of constraints, each involving two variables, where each variable ranges over a set of…
Let $\Sigma$ be an alphabet. For two strings $X$, $Y$, and a constrained string $P$ over the alphabet $\Sigma$, the constrained longest common subsequence and substring problem for two strings $X$ and $Y$ with respect to $P$ is to find a…
In the trace reconstruction problem, one seeks to reconstruct a binary string $s$ from a collection of traces, each of which is obtained by passing $s$ through a deletion channel. It is known that $\exp(\tilde O(n^{1/5}))$ traces suffice to…
The compressed indexing problem is to preprocess a string $S$ of length $n$ into a compressed representation that supports pattern matching queries. That is, given a string $P$ of length $m$ report all occurrences of $P$ in $S$. We present…
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…
A classical measure of string comparison is given by the longest common subsequence (LCS) problem on a pair of strings. We consider its generalisation, called the semi-local LCS problem, which arises naturally in many string-related…
A $t$-covering array with entries from the alphabet ${\cal Q}=\{0,1,\ldots,q-1\}$ is a $k\times n$ stack, so that for any choice of $t$ (typically non-consecutive) columns, each of the $q^{t}$ possible $t$-letter words over ${\cal Q}$…
In this paper we define a new problem, motivated by computational biology, $LCSk$ aiming at finding the maximal number of $k$ length $substrings$, matching in both input strings while preserving their order of appearance. The traditional…
We study regular expression membership testing: Given a regular expression of size $m$ and a string of size $n$, decide whether the string is in the language described by the regular expression. Its classic $O(nm)$ algorithm is one of the…
The longest common subsequence (LCS) is a fundamental problem in string processing which has numerous algorithmic studies, extensions, and applications. A sequence $u_1, \ldots, u_f$ of $f$ strings s said to be an ($f$-)segmentation of a…
Word Break is a prototypical factorization problem in string processing: Given a word $w$ of length $N$ and a dictionary $\mathcal{D} = \{d_1, d_2, \ldots, d_{K}\}$ of $K$ strings, determine whether we can partition $w$ into words from…
A \itbf{cover} of a string $x = x[1..n]$ is a proper substring $u$ of $x$ such that $x$ can be constructed from possibly overlapping instances of $u$. A recent paper \cite{FIKPPST13} relaxes this definition --- an \itbf{enhanced cover} $u$…
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…