Related papers: Duplication with transposition distance to the roo…
We study the space requirements of a sorting algorithm where only items that at the end will be adjacent are kept together. This is equivalent to the following combinatorial problem: Consider a string of fixed length n that starts as a…
Hairpin completion, derived from the hairpin formation observed in DNA biochemistry, is an operation applied to strings, particularly useful in DNA computing. Conceptually, a right hairpin completion operation transforms a string $S$ into…
An (n,d) permutation array (PA) is a set of permutations of length n with the property that the distance (under some metric) between any two permutations in the array is at least d. They became popular recently for communication over power…
This paper is concerned with practical implementations of approximate string dictionaries that allow edit errors. In this problem, we have as input a dictionary $D$ of $d$ strings of total length $n$ over an alphabet of size $\sigma$. Given…
The normalized edit distance is one of the distances derived from the edit distance. It is useful in some applications because it takes into account the lengths of the two strings compared. The normalized edit distance is not defined in…
We investigate the asymptotic standard deviation of the Longest Common Subsequence (LCS) of two independent i.i.d. sequences of length n. The first sequence is drawn from a three letter alphabet {0,1,a}, whilst the second sequence is…
In the deletion channel, an important problem is to determine the number of subsequences derived from a string $U$ of length $n$ when subjected to $t$ deletions. It is well-known that the number of subsequences in the setting exhibits a…
A permutation array $A$ is a set of permutations on a finite set $\Omega$, say of size $n$. Given distinct permutations $\pi, \sigma\in \Omega$, we let $hd(\pi, \sigma) = |\{ x\in \Omega: \pi(x) \ne \sigma(x) \}|$, called the Hamming…
Let $\Omega_n$ be the family of binary trees on $n$ vertices obtained by identifying the root of an rgood binary tree with a vertex of maximum eccentricity of a binary caterpillar. In the paper titled "On different middle parts of a tree…
Let $p$ be an odd prime and $r,s,m$ be positive integers. In this study, we initiate our exploration by delving into the intricate structure of all repeated-root cyclic codes and their duals with a length of $2^rp^s$ over the finite field…
In this paper we study a variation of the accessibility percolation model, this is also motivated by evolutionary biology and evolutionary computation. Consider a tree whose vertices are labeled with random numbers. We study the probability…
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 study the list-decoding problem of alternant codes, with the notable case of classical Goppa codes. The major consideration here is to take into account the size of the alphabet, which shows great influence on the list-decoding radius.…
String consensus problems aim at finding a string that minimizes some given distance with respect to an input set of strings. In particular, in the Closest string problem, we are given a set of strings of equal length and a radius $d$. The…
We present an algorithm for approximating the edit distance between two strings of length $n$ in time $n^{1+\varepsilon}$ up to a constant factor, for any $\varepsilon>0$. Our result completes a research direction set forth in the recent…
The problem of finding a center string that is `close' to every given string arises and has many applications in computational biology and coding theory. This problem has two versions: the Closest String problem and the Closest Substring…
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…
In distance query reconstruction, we wish to reconstruct the edge set of a hidden graph by asking as few distance queries as possible to an oracle. Given two vertices $u$ and $v$, the oracle returns the shortest path distance between $u$…
The Pr\"ufer code is a bijection between trees on the vertex set $[n]$ and strings on the set $[n]$ of length $n-2$ (Pr\"ufer strings of order $n$). In this paper we examine the `locality' properties of the Pr\"ufer code, i.e. the effect of…
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,…