Related papers: Minimal unique palindromic substrings after single…
Countless variants of the Lempel-Ziv compression are widely used in many real-life applications. This paper is concerned with a natural modification of the classical pattern matching problem inspired by the popularity of such compression…
In this paper, we introduce new types of approximate palindromes called single-arm-gapped palindromes (shortly SAGPs). A SAGP contains a gap in either its left or right arm, which is in the form of either $wguc u^R w^R$ or $wuc u^Rgw^R$,…
We consider the approximate pattern matching problem under the edit distance. Given a text $T$ of length $n$, a pattern $P$ of length $m$, and a threshold $k$, the task is to find the starting positions of all substrings of $T$ that can be…
We propose algorithms that, given the input string of length $n$ over integer alphabet of size $\sigma$, construct the Burrows-Wheeler transform (BWT), the permuted longest-common-prefix (PLCP) array, and the LZ77 parsing in…
We consider computing a longest palindrome in the streaming model, where the symbols arrive one-by-one and we do not have random access to the input. While computing the answer exactly using sublinear space is not possible in such a…
Lately, there is a growing interest in dynamic string matching problems. Specifically, the dynamic Longest Common Factor problem has been researched and some interesting results has been reached. In this paper we examine another classic…
A weighted string, also known as a position weight matrix, is a sequence of probability distributions over some alphabet. We revisit the Weighted Shortest Common Supersequence (WSCS) problem, introduced by Amir et al. [SPIRE 2011], that is,…
Given a string $s$ of length $n$ over a general alphabet and an integer $k$, the problem is to decide whether $s$ is a concatenation of $k$ nonempty palindromes. Two previously known solutions for this problem work in time $O(kn)$ and…
In this paper, we consider a generalized longest common subsequence problem with multiple substring inclusive constraints. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constraints $P=\{P_1,\cdots,P_d\}$…
In this paper we study the fundamental problem of maintaining a dynamic collection of strings under the following operations: concat - concatenates two strings, split - splits a string into two at a given position, compare - finds the…
Given two strings $T$ and $S$ and a set of strings $P$, for each string $p \in P$, consider the unique substrings of $T$ that have $p$ as their prefix and $S$ as their suffix. Two problems then come to mind; the first problem being the…
Given a string $S$ of length $n$, the classic string indexing problem is to preprocess $S$ into a compact data structure that supports efficient subsequent pattern queries. In the \emph{deterministic} variant the goal is to solve the string…
Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using a…
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…
The longest square subsequence (LSS) problem consists of computing a longest subsequence of a given string $S$ that is a square, i.e., a longest subsequence of form $XX$ appearing in $S$. It is known that an LSS of a string $S$ of length…
In the Pattern Masking for Dictionary Matching (PMDM) problem, we are given a dictionary $\mathcal{D}$ of $d$ strings, each of length $\ell$, a query string $q$ of length $\ell$, and a positive integer $z$, and we are asked to compute a…
We consider the $Parameterized$ $Pattern$ $Matching$ problem, where a pattern $P$ matches some location in a text $\mathsf{T}$ iff there is a one-to-one correspondence between the alphabet symbols of the pattern to those of the text. More…
The classic string indexing problem is to preprocess a string S into a compact data structure that supports efficient pattern matching queries. Typical queries include existential queries (decide if the pattern occurs in S), reporting…
A binary matrix has the Consecutive Ones Property (C1P) if its columns can be ordered in such a way that all 1s on each row are consecutive. These matrices are used for DNA physical mapping and ancestral genome reconstruction in…
Given a sequence $S$ of length $n$, a letter-duplicated subsequence is a subsequence of $S$ in the form of $x_1^{d_1}x_2^{d_2}\cdots x_k^{d_k}$ with $x_i\in\Sigma$, $x_j\neq x_{j+1}$ and $d_i\geq 2$ for all $i$ in $[k]$ and $j$ in $[k-1]$.…