Related papers: Duplication with transposition distance to the roo…
We study the tandem duplication distance between binary sequences and their roots. In other words, the quantity of interest is the number of tandem duplication operations of the form $\seq x = \seq a \seq b \seq c \to \seq y = \seq a \seq b…
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 set of all $ q $-ary strings that do not contain repeated substrings of length $ \leqslant\! 3 $ (i.e., that do not contain substrings of the form $ a a $, $ a b a b $, and $ a b c a b c $) constitutes a code correcting an arbitrary…
On the string of finite length, a (genomic) transposition is defined as the operation of exchanging two consecutive substrings. The minimum number of transpositions needed to transform one into the other is the transposition distance, that…
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…
The problem of correcting transpositions (or swaps) of consecutive symbols in $ q $-ary strings is studied. Lower bounds on asymptotically achievable rates of codes correcting $ t = \tau n $ transpositions are derived. The first bound is…
A $q$-ary maximum distance separable (MDS) code $C$ with length $n$, dimension $k$ over an alphabet $\mathcal{A}$ of size $q$ is a set of $q^k$ codewords that are elements of $\mathcal{A}^n$, such that the Hamming distance between two…
Motivated by DNA storage in living organisms, and by known biological mutation processes, we study the reverse-complement string-duplication system. We fully classify the conditions under which the system has full expressiveness, for all…
We find exact and asymptotic formulas for the number of pairs $(p,q)$ of $N$-cycles such that the all cycles of the product $p\cdot q$ have lengths from a given integer set. We then apply these results to prove a surprisingly high lower…
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…
The Swap-Insert Correction distance from a string $S$ of length $n$ to another string $L$ of length $m\geq n$ on the alphabet $[1..d]$ is the minimum number of insertions, and swaps of pairs of adjacent symbols, converting $S$ into $L$.…
We consider the problem of constructing a code capable of correcting a single long tandem duplication error of variable length. As the main contribution of this paper, we present a $q$-ary efficiently encodable code of length $n+1$ and…
We study codes that can correct backtracking errors during nanopore sequencing. In this channel, a sequence of length $n$ over an alphabet of size $q$ is being read by a sliding window of length $\ell$, where from each window we obtain only…
Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…
Non-overlapping codes are a set of codewords such that the prefix of each codeword is not a suffix of any codeword in the set, including itself. If the lengths of the codewords are variable, it is additionally required that every codeword…
A two-dimensional string is simply a two-dimensional array. We continue the study of the combinatorial properties of repetitions in such strings over the binary alphabet, namely the number of distinct tandems, distinct quartics, and runs.…
Let A(q,n,d) denote the maximum size of a q-ary code of length n and distance d. We study the minimum asymptotic redundancy \rho(q,n,d)=n-log_q A(q,n,d) as n grows while q and d are fixed. For any d and q<=d-1, long algebraic codes are…
We study the maximum length of $q$-ary codes as a function of alphabet size, code size, and Singleton defect. For an $(n, M, d)_q$ code with dimension $\kappa = \log_q M \ge 2$ and Singleton defect $s = n - \lceil\kappa\rceil + 1 - d$, we…
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…