Related papers: On the Palindromic/Reverse-Complement Duplication …
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…
With distributed computing and mobile applications becoming ever more prevalent, synchronizing diverging replicas of the same data is a common problem. Reconciliation -- bringing two replicas of the same data structure as close as possible…
This paper investigates the problem of correcting multiple criss-cross insertions and deletions in arrays. More precisely, we study the unique recovery of $n \times n$ arrays affected by $t$-criss-cross deletions defined as any combination…
In this work, we investigate a challenging problem, which has been considered to be an important criterion in designing codewords for DNA computing purposes, namely secondary structure avoidance in single-stranded DNA molecules. In short,…
Reed-Muller codes are some of the oldest and most widely studied error-correcting codes, of interest for both their algebraic structure as well as their many algorithmic properties. A recent beautiful result of Saptharishi, Shpilka and Volk…
The problem of correcting deletions and insertions has recently received significantly increased attention due to the DNA-based data storage technology, which suffers from deletions and insertions with extremely high probability. In this…
An exact-match overlap graph of $n$ given strings of length $\ell$ is an edge-weighted graph in which each vertex is associated with a string and there is an edge $(x,y)$ of weight $\omega = \ell - |ov_{max}(x,y)|$ if and only if $\omega…
We prove that certain classical cyclic redundancy check codes can be used for classical error correction and not just classical error detection. We extend the idea of classical cyclic redundancy check codes to quantum cyclic redundancy…
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…
In this paper, we study codes correcting $t$ duplications of $\ell$ consecutive symbols. These errors are known as tandem duplication errors, where a sequence of symbols is repeated and inserted directly after its original occurrence. Using…
The problem of correcting deletions has received significant attention, partly because of the prevalence of these errors in DNA data storage. In this paper, we study the problem of correcting a consecutive burst of at most $t$ deletions in…
We introduce alphabet-permutation (AP) codes, a new family of error-correcting codes defined by iteratively applying random coordinate-wise permutations to a fixed initial word. A special case recovers random additive codes and random…
In this paper, we show that the single deletion correcting Varshamov-Tenengolts code, with minor modifications, can also correct an ordered deletion-erasure pattern where one deletion and at most one erasure occur and the deletion always…
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…
A simple construction of quaternary hermitian self-orthogonal codes with parameters $[2n+1,k+1]$ and $[2n+2,k+2]$ from a given pair of self-orthogonal $[n,k]$ codes, and its link to quantum codes is considered. As an application, an optimal…
Codes for correcting sticky insertions/deletions and limited-magnitude errors have attracted significant attention due to their applications of flash memories, racetrack memories, and DNA data storage systems. In this paper, we first…
Maximum run-length limited codes are constraint codes used in communication and data storage systems. Insertion/deletion correcting codes correct insertion or deletion errors caused in transmitted sequences and are used for combating…
DNA codes have many applications, such as in data storage, DNA computing, etc. Good DNA codes have large sizes and satisfy some certain constraints. In this paper, we present a new construction method for reversible DNA codes. We show that…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
The sequence reconstruction problem, introduced by Levenshtein in 2001, considers a communication scenario where the sender transmits a codeword from some codebook and the receiver obtains multiple noisy reads of the codeword. The common…