Related papers: Closed Repeats
Merging $T$ sorted, non-redundant lists containing $M$ elements into a single sorted, non-redundant result of size $N \ge M/T$ is a classic problem typically solved practically in $O(M \log T)$ time with a priority-queue data structure the…
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…
One of the most fundamental method for comparing two given strings $A$ and $B$ is the longest common subsequence (LCS), where the task is to find (the length) of an LCS of $A$ and $B$. In this paper, we deal with the STR-IC-LCS problem…
Let $S_n$ denote the set of permutations of $[n]$ and let $\sigma=\sigma_1\cdots\sigma_n\in S_n$. For a subsequence $\{\sigma_{i_j}\}_{j=1}^k$ of $\{\sigma_i\}_{i=1}^n$ of length $k\ge2$, construct the ``up/down'' sequence $V_1\cdots…
The all-pairs suffix-prefix (APSP) problem is a classical problem in string processing which has important applications in bioinformatics. Given a set $\mathcal{S} = \{S_1, \ldots, S_k\}$ of $k$ strings, the APSP problem asks one to compute…
We study here the so called subsequence pattern matching also known as hidden pattern matching in which one searches for a given pattern $w$ of length $m$ as a subsequence in a random text of length $n$. The quantity of interest is the…
A superpermutation is a sequence that contains every permutation of $n$ distinct symbols as a contiguous substring. For instance, a valid example for three symbols is a sequence that contains all six permutations. This paper introduces a…
Two strings of the same length are said to Cartesian-tree match (CT-match) if their Cartesian-trees are isomorphic [Park et al., TCS 2020]. Cartesian-tree matching is a natural model that allows for capturing similarities of numerical…
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…
In grammar-based compression a string is represented by a context-free grammar, also called a straight-line program (SLP), that generates only that string. We refine a recent balancing result stating that one can transform an SLP of size…
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…
Suppose we are asked to preprocess a string \(s [1..n]\) such that later, given a substring's endpoints, we can quickly count how many distinct characters it contains. In this paper we give a data structure for this problem that takes \(n…
Approximate string matching is the problem of finding all factors of a text t of length n that are at a distance at most k from a pattern x of length m. Approximate circular string matching is the problem of finding all factors of t that…
We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with $p$ processors. Given a static text of length $n$, we first show how to compute the suffix array interval of a given…
Given the query string of length $m$, we explore a parallel query in a static suffix tree based data structure for $p \ll n$, where $p$ is the number of processors and $n$ is the length of the text. We present three results on CREW PRAM.…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
We consider the longest common subsequence problem in the context of subsequences with gap constraints. In particular, following Day et al. 2022, we consider the setting when the distance (i. e., the gap) between two consecutive symbols of…
Real-world data often comes in compressed form. Analyzing compressed data directly (without decompressing it) can save space and time by orders of magnitude. In this work, we focus on fundamental sequence comparison problems and try to…
The problem of reconstructing strings from their substring spectra has a long history and in its most simple incarnation asks for determining under which conditions the spectrum uniquely determines the string. We study the problem of coded…
In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…