Related papers: On the Palindromic/Reverse-Complement Duplication …
In the modern era of large-scale computing systems, a crucial use of error correcting codes is to judiciously introduce redundancy to ensure recoverability from failure. To get the most out of every byte, practitioners and theorists have…
Insertion-deletion codes (insdel codes for short) are used for correcting synchronization errors in communications, and in other many interesting fields such as DNA storage, date analysis, race-track memory error correction and language…
We consider the problem of constructing codes that can correct $\delta$ deletions occurring in an arbitrary binary string of length $n$ bits. Varshamov-Tenengolts (VT) codes, dating back to 1965, are zero-error single deletion $(\delta=1)$…
One peculiarity with deletion-correcting codes is that perfect $t$-deletion-correcting codes of the same length over the same alphabet can have different numbers of codewords, because the balls of radius $t$ with respect to the…
A composition of a nonnegative integer (n) is a sequence of positive integers whose sum is (n). A composition is palindromic if it is unchanged when its terms are read in reverse order. We provide a generating function for the number of…
We construct deletion error-correcting codes in the oblivious model, where errors are adversarial but oblivious to the encoder's randomness. Oblivious errors bridge the gap between the adversarial and random error models, and are motivated…
This paper concerns non-overlapping codes, block codes motivated by synchronisation and DNA-based storage applications. Most existing constructions of these codes do not account for the restrictions posed by the physical properties of…
A quasi-Gray code of dimension $n$ and length $\ell$ over an alphabet $\Sigma$ is a sequence of distinct words $w_1,w_2,\dots,w_\ell$ from $\Sigma^n$ such that any two consecutive words differ in at most $c$ coordinates, for some fixed…
In 2007, Martinian and Trott presented codes for correcting a burst of erasures with a minimum decoding delay. Their construction employs [n,k] codes that can correct any burst of erasures (including wrap-around bursts) of length n-k. The…
We construct codes over the ring $\mathbb{F}_2+u\mathbb{F}_2$ with $u^2=0$. These code are designed for use in DNA computing applications. The codes obtained satisfy the reverse complement constraint, the $GC$ content constraint and avoid…
In the usual trace reconstruction problem, the goal is to exactly reconstruct an unknown string of length $n$ after it passes through a deletion channel many times independently, producing a set of traces (i.e., random subsequences of the…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
A palindrome is a string that reads the same forward and backward. A palindromic substring $w$ of a string $T$ is called a minimal unique palindromic substring (MUPS) of $T$ if $w$ occurs only once in $T$ and any proper palindromic…
A complementary Gray code for binary n-tuples is one that, when all the tuples are complemented, is identical to itself; this is equivalent to the complement of the first half of the code being identical to the second half. We generalize…
In the paper, the Levenshtein's sequence reconstruction problem is considered in the case where at most $t$ substitution errors occur in each of the $N$ channels and the decoder outputs a list of length $\mathcal{L}$. Moreover, it is…
We improve the upper bound of Levenshtein for the cardinality of a code of length 4 capable of correcting single deletions over an alphabet of even size. We also illustrate that the new upper bound is sharp. Furthermore we will construct an…
This paper extends the problem of 2-dimensional palindrome search into the area of approximate matching. Using the Hamming distance as the measure, we search for 2D palindromes that allow up to $k$ mismatches. We consider two different…
In this paper, we present an explicit construction of list-decodable codes for single-deletion and single-substitution with list size two and redundancy 3log n+4, where n is the block length of the code. Our construction has lower…
We prove that a binary linear code of block length $n$ that is locally correctable with $3$ queries against a fraction $\delta > 0$ of adversarial errors must have dimension at most $O_{\delta}(\log^2 n \cdot \log \log n)$. This is almost…
The analysis of the decoding failure rate of the bit-flipping algorithm has received increasing attention. For a binary linear code we consider the minimum number of rows in a parity-check matrix such that the bit-flipping algorithm is able…