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A $q$-ary code of length $n$, size $M$, and minimum distance $d$ is called an $(n,M,d)_q$ code. An $(n,q^{k},n-k+1)_q$ code is called a maximum distance separable (MDS) code. In this work, some MDS codes over small alphabets are classified.…
We consider the classical exact multiple string matching problem. Our solution is based on $q$-grams combined with pattern superimposition, bit-parallelism and alphabet size reduction. We discuss the pros and cons of the various…
For an integer $q\ge 2$ and an even integer $d$, consider the graph obtained from a large complete $q$-ary tree by connecting with an edge any two vertices at distance exactly $d$ in the tree. This graph has clique number $q+1$, and the…
We consider an efficient two-party protocol for securely computing the similarity of strings w.r.t. an extended edit distance measure. Here, two parties possessing strings $x$ and $y$, respectively, want to jointly compute an approximate…
The edit distance is a way of quantifying how similar two strings are to one another by counting the minimum number of character insertions, deletions, and substitutions required to transform one string into the other. In this paper we…
A permutation array(or code) of length $n$ and distance $d$, denoted by $(n,d)$ PA, is a set of permutations $C$ from some fixed set of $n$ elements such that the Hamming distance between distinct members $\mathbf{x},\mathbf{y}\in C$ is at…
The main conjecture on maximum distance separable (MDS) codes states that, execpt for some special cases, the maximum length of a q-ary linear MDS code is q+1. This conjecture does not hold true for near maximum distance separable codes…
A reformulation of the path length of binary search trees is given in terms of permutations, allowing to extend the definition to the instance of words, where the letters are obtained by independent geometric random variables (with…
Motivated by applications in in-vivo DNA storage, we study codes for correcting duplications. A reverse-complement duplication of length $k$ is the insertion of the reversed and complemented copy of a substring of length $k$ adjacent to its…
Computing string or sequence alignments is a classical method of comparing strings and has applications in many areas of computing, such as signal processing and bioinformatics. Semi-local string alignment is a recent generalisation of this…
The trace reconstruction problem studies the number of noisy samples needed to recover an unknown string $\boldsymbol{x}\in\{0,1\}^n$ with high probability, where the samples are independently obtained by passing $\boldsymbol{x}$ through a…
Computing the edit distance of two strings is one of the most basic problems in computer science and combinatorial optimization. Tree edit distance is a natural generalization of edit distance in which the task is to compute a measure of…
Cyclic codes are the most studied subclass of linear codes and widely used in data storage and communication systems. Many cyclic codes have optimal parameters or the best parameters known. They are divided into simple-root cyclic codes and…
Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…
The edit distance is a basic string similarity measure used in many applications such as text mining, signal processing, bioinformatics, and so on. However, the computational cost can be a problem when we repeat many distance calculations…
Let $X=X(n,q)$ be the set of $n\times n$ Hermitian matrices over $\mathbb{F}_{q^2}$. It is well known that $X$ gives rise to a metric translation association scheme whose classes are induced by the rank metric. We study $d$-codes in this…
In this paper we prove new lower bounds for the maximal size of permutation codes by connecting the theory of permutation codes with the theory of linear block codes. More specifically, using the columns of a parity check matrix of an…
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…
Due to its high data density and longevity, DNA is considered a promising medium for satisfying ever-increasing data storage needs. However, the diversity of errors that occur in DNA sequences makes efficient error-correction a challenging…
This thesis investigates three biologically inspired operations: prefix-suffix duplication, bounded prefix-suffix duplication, and prefix-suffix-square completion. Duplication, a common genetic mutation, involves repeating DNA sequences and…