Related papers: Duplication with transposition distance to the roo…
Repeat finding in strings has important applications in subfields such as computational biology. Surprisingly, all prior work on repeat finding did not consider the constraint on the locality of repeats. In this paper, we propose and study…
The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants…
Although real-world text datasets, such as DNA sequences, are far from being uniformly random, average-case string searching algorithms perform significantly better than worst-case ones in most applications of interest. In this paper, we…
The $q$-ary block codes with two distances $d$ and $d+1$ are considered. Several constructions of such codes are given, as in the linear case all codes can be obtained by a simple modification of linear equidistant codes. Upper bounds for…
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…
Explicit non-asymptotic upper bounds on the sizes of multiple-deletion correcting codes are presented. In particular, the largest single-deletion correcting code for $q$-ary alphabet and string length $n$ is shown to be of size at most…
A basic problem for constant dimension codes is to determine the maximum possible size $A_q(n,d;k)$ of a set of $k$-dimensional subspaces in $\mathbb{F}_q^n$, called codewords, such that the subspace distance satisfies…
Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…
In this work, we consider the problem of pattern matching under the dynamic time warping (DTW) distance motivated by potential applications in the analysis of biological data produced by the third generation sequencing. To measure the DTW…
Several measures exist for string similarity, including notable ones like the edit distance and the indel distance. The former measures the count of insertions, deletions, and substitutions required to transform one string into another,…
We present the first dynamic algorithms for Dyck and tree edit distances with subpolynomial update times. Dyck edit distance measures how far a parenthesis string is from a well-parenthesized expression, while tree edit distance quantifies…
Nanopore sequencing is a promising technology for DNA sequencing. In this paper, we investigate a specific model of the nanopore sequencer, which takes a $q$-ary sequence of length $n$ as input and outputs a vector of length $n+\ell-1$…
It was shown in \cite{GXY18} that the length $n$ of a $q$-ary linear locally recoverable code with distance $d\ge 5$ is upper bounded by $O(dq^3)$. Thus, it is a challenging problem to construct $q$-ary locally recoverable codes with…
Three standard subtree transfer operations for binary trees, used in particular for phylogenetic trees, are: tree bisection and reconnection ($TBR$), subtree prune and regraft ($SPR$) and rooted subtree prune and regraft ($rSPR$). For a…
For $q$-ary $n$-sequences, we develop the concept of similarity functions that can be used (for $q=4$) to model a thermodynamic similarity on DNA sequences. A similarity function is identified by the length of a longest common subsequence…
Both MDS and Euclidean self-dual codes have theoretical and practical importance and the study of MDS self-dual codes has attracted lots of attention in recent years. In particular, determining existence of $q$-ary MDS self-dual codes for…
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…
We study error-correcting codes in the space $\mathcal{S}_{n,q}$ of length-$n$ multisets over a $q$-ary alphabet, motivated by permutation channels in which ordering is completely lost and errors act solely by deletions of symbols, i.e., by…
Given two binary trees on $N$ labeled leaves, the quartet distance between the trees is the number of disagreeing quartets. By permuting the leaves at random, the expected quartets distance between the two trees is…
An orientable sequence of order $n$ over an alphabet $\{0,1,\ldots, k{-}1\}$ is a cyclic sequence such that each length-$n$ substring appears at most once \emph{in either direction}. When $k= 2$, efficient algorithms are known to construct…