Related papers: Semi-local string comparison: algorithmic techniqu…

The 2-LCPS problem, first introduced by Chowdhury et al. [Fundam. Inform., 129(4):329-340, 2014], asks one to compute (the length of) a longest palindromic common subsequence between two given strings $A$ and $B$. We show that the 2-LCPS…

The problem of finding longest common subsequence (LCS) is one of the fundamental problems in computer science, which finds application in fields such as computational biology, text processing, information retrieval, data compression etc.…

String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…

This note provides very simple, efficient algorithms for computing the number of distinct longest common subsequences of two input strings and for computing the number of LCS embeddings.

Given two sequences $A[1..n]$ and $B[1..m]$ over a totally ordered alphabet, the \emph{Longest Common Bitonic Subsequence} (LCBS) problem asks for a longest common subsequence that is strictly increasing up to a single peak element and…

Sequence comparison is a widely used computational technique in modern molecular biology. In spite of the frequent use of sequence comparisons the important problem of assigning statistical significance to a given degree of similarity is…

Maximal Common Subsequences (MCSs) between two strings X and Y are subsequences of both X and Y that are maximal under inclusion. MCSs relax and generalize the well known and widely used concept of Longest Common Subsequences (LCSs), which…

The Longest Common Substring (LCS) and Longest Palindromic Substring (LPS) are classical problems in computer science, representing fundamental challenges in string processing. Both problems can be solved in linear time using a classical…

The approximate string matching is a fundamental and recurrent problem that arises in most computer science fields. This problem can be defined as follows: Let $D=\{x_1,x_2,\ldots x_d\}$ be a set of $d$ words defined on an alphabet…

We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…

We consider the problem of finding, given two documents of total length $n$, a longest string occurring as a substring of both documents. This problem, known as the Longest Common Substring (LCS) problem, has a classic $O(n)$-time solution…

Due to the increased availability of large datasets of biological sequences, the tools for sequence comparison are now relying on efficient alignment-free approaches to a greater extent. Most of the alignment-free approaches require the…

We give a near-optimal quantum algorithm for the longest common substring (LCS) problem between two run-length encoded (RLE) strings, with the assumption that the prefix-sums of the run-lengths are given. Our algorithm costs…

In the Manhattan Sequence Consensus problem (MSC problem) we are given $k$ integer sequences, each of length $l$, and we are to find an integer sequence $x$ of length $l$ (called a consensus sequence), such that the maximum Manhattan…

In this paper, we consider a generalized longest common subsequence problem with multiple substring exclusion constrains. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constrains $P=\{P_1,...,P_d\}$ of…

Classic similarity measures of strings are longest common subsequence and Levenshtein distance (i.e., the classic edit distance). A classic similarity measure of curves is dynamic time warping. These measures can be computed by simple…

The Average Common Substring (ACS) is a popular alignment-free distance measure for phylogeny reconstruction. The ACS can be computed in O(n) space and time, where n=x+y is the input size. The compressed string matching is the study of…

Non-parametric entropy estimation on sequential data is a fundamental tool in signal processing, capturing information flow within or between processes to measure predictability, redundancy, or similarity. Methods based on longest common…

The {\em shortest common superstring} and the {\em shortest common supersequence} are two well studied problems having a wide range of applications. In this paper we consider both problems with resource constraints, denoted as 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…