Related papers: Reconstruction of Sequences Distorted by Two Inser…
The interest in channel models in which the data is sent as an unordered set of binary strings has increased lately, due to emerging applications in DNA storage, among others. In this paper we analyze the minimal redundancy of binary codes…
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…
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.…
Levenshtein first introduced the sequence reconstruction problem in $2001$. In the realm of combinatorics, the sequence reconstruction problem is equivalent to determining the value of $N(n,d,t)$, which represents the maximum size of the…
This paper studies the sequence reconstruction problem for a channel inspired by protein identification. We introduce a coloring channel, where a sequence is transmitted through a channel that deletes all symbols not belonging to a fixed…
In this paper, we investigate binary reconstruction codes capable of correcting one deletion and one substitution. We define the \emph{single-deletion single-substitution ball} function $ \mathcal{B} $ as a mapping from a sequence to the…
Motivated by average-case trace reconstruction and coding for portable DNA-based storage systems, we initiate the study of \emph{coded trace reconstruction}, the design and analysis of high-rate efficiently encodable codes that can be…
We consider the problem of storing and retrieving information from synthetic DNA media. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on their collection of substrings…
We consider the problem of constructing binary codes to recover from $k$-bit deletions with efficient encoding/decoding, for a fixed $k$. The single deletion case is well understood, with the Varshamov-Tenengolts-Levenshtein code from 1965…
We first give a construction of binary $t_1$-deletion-$t_2$-insertion-burst correcting codes with redundancy at most $\log(n)+(t_1-t_2-1)\log\log(n)+O(1)$, where $t_1\ge 2t_2$. Then we give an improved construction of binary codes capable…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
Nanopore sequencing, superior to other sequencing technologies for DNA storage in multiple aspects, has recently attracted considerable attention. Its high error rates, however, demand thorough research on practical and efficient coding…
In this paper, we consider the Levenshtein's sequence reconstruction problem in the case where the transmitted codeword is chosen from $\{0,1\}^n$ and the channel can delete up to $t$ symbols from the transmitted codeword. We determine the…
Regenerating codes allow distributed storage systems to recover from the loss of a storage node while transmitting the minimum possible amount of data across the network. We present a systematic computer search for optimal systematic…
The prevalent technique for DNA sequencing consists of two main steps: shotgun sequencing, where many randomly located fragments, called reads, are extracted from the overall sequence, followed by an assembly algorithm that aims to…
We consider the problem of assembling a sequence based on a collection of its substrings observed through a noisy channel. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on…
An edit refers to a single insertion, deletion, or substitution. This paper aims to construct binary codes that can correct two edits. To do this, a necessary and sufficient condition for a code to be two-edit correctable is provided,…
Sequencing a DNA strand, as part of the read process in DNA storage, produces multiple noisy copies which can be combined to produce better estimates of the original strand; this is called trace reconstruction. One can reduce the error rate…
Erasure codes are an efficient means of storing data across a network in comparison to data replication, as they tend to reduce the amount of data stored in the network and offer increased resilience in the presence of node failures. The…
This paper studies codes that correct bursts of deletions. Namely, a code will be called a $b$-burst-deletion-correcting code if it can correct a deletion of any $b$ consecutive bits. While the lower bound on the redundancy of such codes…