相关论文: Duplication Distance to the Root for Binary Sequen…
We study the duplication with transposition distance between strings of length $n$ over a $q$-ary alphabet and their roots. In other words, we investigate the number of duplication operations of the form $x = (abcd) \to y = (abcbd)$, where…
A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…
In computational biology, tandem duplication is an important biological phenomenon which can occur either at the genome or at the DNA level. A tandem duplication takes a copy of a genome segment and inserts it right after the segment - this…
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 discrepancy of a binary string refers to the maximum (absolute) difference between the number of ones and the number of zeroes over all possible substrings of the given binary string. We provide an investigation of the discrepancy of…
The construction of self-dual codes over small fields such that their minimum distances are as large as possible is a long-standing challenging problem in the coding theory. In 2009, a family of binary self-dual cyclic codes with lengths…
Tandem duplication in DNA 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 {\em et al.} (2016) proposed the study of codes that…
Binary cyclic codes are worth studying due to their applications and theoretical importance. It is an important problem to construct an infinite family of cyclic codes with large minimum distance $d$ and dual distance $d^{\perp}$. In recent…
Given a set of sequences, the distance between pairs of them helps us to find their similarity and derive structural relationship amongst them. For genomic sequences such measures make it possible to construct the evolution tree of…
As well known the rotation distance D(S,T) between two binary trees S, T of n vertices is the minimum number of rotations of pairs of vertices to transform S into T. We introduce the new operation of chain rotation on a tree, involving two…
In this paper, the construction of finite-length binary sequences whose nonlinear complexity is not less than half of the length is investigated. By characterizing the structure of the sequences, an algorithm is proposed to generate all…
Due to its high data density and longevity, DNA is considered a promising medium for satisfying ever-increasing data storage needs. However, the diversity of errors that occur in DNA sequences makes efficient error-correction a challenging…
A (tandem) duplication of length $ k $ is an insertion of an exact copy of a substring of length $ k $ next to its original position. This and related types of impairments are of relevance in modeling communication in the presence of…
We classify all binary error correcting completely regular codes of length $n$ with minimum distance $\delta>n/2$.
We devise an analytically simple as well as invertible approximate expression, which describes the relation between the minimum distance of a binary code and the corresponding maximum attainable code-rate. For example, for a rate-(1/4),…
Tandem duplication is an evolutionary process whereby a segment of DNA is replicated and proximally inserted. The different configurations that can arise from this process give rise to some interesting combinatorial questions. Firstly, we…
We study the problem of aligning multiple sequences with the goal of finding an alignment that either maximizes the number of aligned symbols (the longest common subsequence (LCS)), or minimizes the number of unaligned symbols (the…
Rotation distance between rooted binary trees is the minimum number of simple rotations needed to transform one tree into the other. Computing the rotation distance between a pair of rooted trees can be quickly reduced in cases where there…
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…
Binary duadic codes are an interesting subclass of cyclic codes since they have large dimensions and their minimum distances may have a square-root bound. In this paper, we present several families of binary duadic codes of length $2^m-1$…