Related papers: Duplication with transposition distance to the roo…
A maximal repetition, or run, in a string, is a maximal periodic substring whose smallest period is at most half the length of the substring. In this paper, we consider runs that correspond to a path on a trie, or in other words, on a…
The edit distance between two rooted ordered trees with $n$ nodes labeled from an alphabet~$\Sigma$ is the minimum cost of transforming one tree into the other by a sequence of elementary operations consisting of deleting and relabeling…
The discrepancy of a binary string is the maximum (absolute) difference between the number of ones and the number of zeroes over all possible substrings of the given binary string. In this note we determine the minimal discrepancy that a…
The Damerau-Levenshtein distance between two sequences is the minimum number of operations (deletions, insertions, substitutions, and adjacent transpositions) required to convert one sequence into another. Notwithstanding a long history of…
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…
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…
Longest common extension queries (often called longest common prefix queries) constitute a fundamental building block in multiple string algorithms, for example computing runs and approximate pattern matching. We show that a sequence of $q$…
Motivated by applications in polymer-based data storage, we study the problem of reconstructing a string from part of its composition multiset. We give a full description of the structure of the strings that cannot be uniquely reconstructed…
The problem of reconstructing a sequence from the set of its length-$k$ substrings has received considerable attention due to its various applications in genomics. We study an uncoded version of this problem where multiple random sources…
In modern storage technologies, symbol-pair codes have emerged as a crucial framework for addressing errors in channels where symbols are read in overlapping pairs to guard against pair errors. A symbol-pair code that meets the…
We present a near-linear time algorithm that approximates the edit distance between two strings within a polylogarithmic factor; specifically, for strings of length n and every fixed epsilon>0, it can compute a (log n)^O(1/epsilon)…
Let $A_q(n,d)$ be the maximum order (maximum number of codewords) of a $q$-ary code of length $n$ and Hamming distance at least $d$. And let $A(n,d,w)$ that of a binary code of constant weight $w$. Building on results from algebraic graph…
In this paper we investigate the \emph{approximate string matching problem} when the allowed edit operations are \emph{non-overlapping unbalanced translocations of adjacent factors}. Such kind of edit operations take place when two adjacent…
In comparative genomics, a transposition is an operation that exchanges two consecutive sequences of genes in a genome. The transposition distance, that is, the minimum number of transpositions needed to transform a genome into another, is,…
Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem…
One peculiarity with deletion-correcting codes is that perfect $t$-deletion-correcting codes of the same length over the same alphabet can have different numbers of codewords, because the balls of radius $t$ with respect to the…
An $n$-ary operation $Q:S^n -> S$ is called an $n$-ary quasigroup of order $|S|$ if in the equation $x_{0}=Q(x_1,...,x_n)$ knowledge of any $n$ elements of $x_0$, ..., $x_n$ uniquely specifies the remaining one. $Q$ is permutably reducible…
We consider a new family of codes, termed asymmetric Lee distance codes, that arise in the design and implementation of DNA-based storage systems and systems with parallel string transmission protocols. The codewords are defined over a…
Starting from a practical use of Reed-Solomon codes in a cryptographic scheme published in Indocrypt'09, this paper deals with the threshold of linear $q$-ary error-correcting codes. The security of this scheme is based on the…
In this paper, we investigate codes designed to correct two bursts of deletions, where each burst has a length of exactly $b$, where $b>1$. The previous best construction, achieved through the syndrome compression technique, had a…