Related papers: String Reconstruction from Substring Compositions
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…
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…
The Shortest Common Superstring (SCS) problem asks for the shortest string that contains each of a given set of strings as a substring. Its reverse-complement variant, the Shortest Common Superstring problem with Reverse Complements…
The Shortest Common Superstring problem (SCS) consists, for a set of strings S = {s_1,...,s_n}, in finding a minimum length string that contains all s_i, 1<= i <= n, as substrings. While a 2+11/30 approximation ratio algorithm has recently…
We propose a list-decoding scheme for reconstruction codes in the context of uniform-tandem-duplication noise, which can be viewed as an application of the associative memory model to this setting. We find the uncertainty associated with…
The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…
A {\it superpattern} is a string of characters of length $n$ that contains as a subsequence, and in a sense that depends on the context, all the smaller strings of length $k$ in a certain class. We prove structural and probabilistic results…
Several recent works have considered the \emph{trace reconstruction problem}, in which an unknown source string $x\in\{0,1\}^n$ is transmitted through a probabilistic channel which may randomly delete coordinates or insert random bits,…
We examine the open problem of finding the shortest string that contains each of the n! permutations of n symbols as contiguous substrings (i.e., the shortest superpermutation on n symbols). It has been conjectured that the shortest…
Consider two or more strings $\mathbf{x}^1,\mathbf{x}^2,\ldots,$ that are concatenated to form $\mathbf{x}=\langle \mathbf{x}^1,\mathbf{x}^2,\ldots \rangle$. Suppose that up to $\delta$ deletions occur in each of the concatenated strings.…
Palindromes are strings that read the same forward and backward. Problems of computing palindromic structures in strings have been studied for many years with a motivation of their application to biology. The longest palindrome problem is…
It is impossible to effectively modify a string in order to increase its Kolmogorov complexity. But is it possible to construct a few strings, not longer than the input string, so that most of them have larger complexity? We show that the…
Maximal repetition of a string is the maximal length of a repeated substring. This paper investigates maximal repetition of strings drawn from stochastic processes. Strengthening previous results, two new bounds for the almost sure growth…
The Shortest Path Reconfiguration problem has as input a graph G (with unit edge lengths) with vertices s and t, and two shortest st-paths P and Q. The question is whether there exists a sequence of shortest st-paths that starts with P and…
We study a variation of the classical Shortest Common Superstring (SCS) problem in which a shortest superstring of a finite set of strings $S$ is sought containing as a factor every string of $S$ or its reversal. We call this problem…
Synthetic polymer-based storage seems to be a particularly promising candidate that could help to cope with the ever-increasing demand for archival storage requirements. It involves designing molecules of distinct masses to represent the…
This paper addresses the problem of finding a representation of a subtree distance, which is an extension of the tree metric. We show that a minimal representation is uniquely determined by a given subtree distance, and give a linear time…
In the trace reconstruction problem, an unknown bit string ${\bf x}\in\{0,1 \}^n$ is sent through a deletion channel where each bit is deleted independently with some probability $q\in(0,1)$, yielding a contracted string $\widetilde{\bf…
The goal of trace reconstruction is to reconstruct an unknown $n$-bit string $x$ given only independent random traces of $x$, where a random trace of $x$ is obtained by passing $x$ through a deletion channel. A Statistical Query (SQ)…
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…