相关论文: Hairpin Completion Distance Lower Bound
In the longest common substring (LCS) problem, we are given two strings $S$ and $T$, each of length at most $n$, and we are asked to find a longest string occurring as a fragment of both $S$ and $T$. This is a classical and well-studied…
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 the problem of estimating the edit distance between two $n$-character strings. While exact computation in the worst case is believed to require near-quadratic time, previous work showed that in certain regimes it is possible to…
We study the problem of computing similarity joins under edit distance on a set of strings. Edit similarity joins is a fundamental problem in databases, data mining and bioinformatics. It finds important applications in data cleaning and…
Identifying palindromes in sequences has been an interesting line of research in combinatorics on words and also in computational biology, after the discovery of the relation of palindromes in the DNA sequence with the HIV virus. Efficient…
We study the fundamental problem of finding the best string to represent a given set, in the form of the Closest String problem: Given a set $X \subseteq \Sigma^d$ of $n$ strings, find the string $x^*$ minimizing the radius of the smallest…
Dynamic Time Warping (DTW) is a widely used similarity measure for comparing strings that encode time series data, with applications to areas including bioinformatics, signature verification, and speech recognition. The standard…
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…
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,…
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…
The edit distance of two strings is the minimum number of insertions, deletions, and substitutions needed to transform one string into the other. The textbook algorithm determines the edit distance of length-$n$ strings in $O(n^2)$ time,…
This study aims to publish a novel similarity metric to increase the speed of comparison operations. Also the new metric is suitable for distance-based operations among strings. Most of the simple calculation methods, such as string length…
We consider the problem of querying a string (or, a database) of length $N$ bits to determine all the locations where a substring (query) of length $M$ appears either exactly or is within a Hamming distance of $K$ from the query. We assume…
A theory is presented of DNA hairpins enclosed in a nanochannel. A hairpin becomes constrained as it approaches the wall of a channel which leads to an entropic force causing the hairpin to tighten. The free energy of the hairpin computed…
Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the string matching problem is a task to find all occurrences of $P$ in $T$. In this study, we propose an algorithm that solves this problem in $O((n + m)q)$ time considering…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behavior of a short RNA or a single stranded DNA molecule that forms hairpin structure and calculate the properties…
Much research in stringology focuses on structures that can, in a way, ``grasp'' repeats (substrings that occur multiple times) as, for example, the so-called runs, a.k.a. maximal repetitions, compactly describe all tandem repeats. In this…
In this paper, we consider the ``Shortest Superstring Problem''(SSP) or the ``Shortest Common Superstring Problem''(SCS). The problem is as follows. For a positive integer $n$, a sequence of n strings $S=(s^1,\dots,s^n)$ is given. We should…
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…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…