相关论文: Hairpin Completion Distance Lower Bound

Hairpin completion and its variant called bounded hairpin completion are operations on formal languages, inspired by a hairpin formation in molecular biology. Another variant called hairpin lengthening has been recently introduced and…

A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…

Hairpin completion is an abstract operation modeling a DNA bio-operation which receives as input a DNA strand $w = x\alpha y \calpha$, and outputs $w' = x \alpha y \bar{\alpha} \bar{x}$, where $\bar{x}$ denotes the Watson-Crick complement…

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…

The edit distance is a fundamental measure of sequence similarity, defined as the minimum number of character insertions, deletions, and substitutions needed to transform one string into the other. Given two strings of length at most $n$,…

The Swap-Insert Correction distance from a string $S$ of length $n$ to another string $L$ of length $m\geq n$ on the alphabet $[1..d]$ is the minimum number of insertions, and swaps of pairs of adjacent symbols, converting $S$ into $L$.…

We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…

The problem of finding a center string that is `close' to every given string arises and has many applications in computational biology and coding theory. This problem has two versions: the Closest String problem and the Closest Substring…

Approximate pattern matching is a natural and well-studied problem on strings: Given a text $T$, a pattern $P$, and a threshold $k$, find (the starting positions of) all substrings of $T$ that are at distance at most $k$ from $P$. We…

The (bounded) hairpin completion and its iterated versions are operations on formal lan- guages which have been inspired by the hairpin formation in DNA-biochemistry. The paper answers two questions asked in the literature about the…

Given two strings $S$ and $P$, the Episode Matching problem is to find the shortest substring of $S$ that contains $P$ as a subsequence. The best known upper bound for this problem is $\tilde O(nm)$ by Das et al. (1997) , where $n,m$ are…

The edit distance (a.k.a. the Levenshtein distance) between two strings is defined as the minimum number of insertions, deletions or substitutions of symbols needed to transform one string into another. The problem of computing the edit…

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…

The algorithmic tasks of computing the Hamming distance between a given pattern of length $m$ and each location in a text of length $n$ is one of the most fundamental algorithmic tasks in string algorithms. Unfortunately, there is evidence…

The hairpin completion is an operation on formal languages that has been inspired by the hairpin formation in DNA biochemistry and by DNA computing. In this paper we investigate the hairpin completion of regular languages. It is well known…

We consider the following model for sampling pairs of strings: $s_1$ is a uniformly random bitstring of length $n$, and $s_2$ is the bitstring arrived at by applying substitutions, insertions, and deletions to each bit of $s_1$ with some…

Pairwise sequence comparison is one of the most fundamental problems in string processing. The most common metric to quantify the similarity between sequences S and T is edit distance, d(S,T), which corresponds to the number of characters…

The Closest String Problem is an NP-hard problem that aims to find a string that has the minimum distance from all sequences that belong to the given set of strings. Its applications can be found in coding theory, computational biology, and…

Text-to-pattern distance is a fundamental problem in string matching, where given a pattern of length $m$ and a text of length $n$, over an integer alphabet, we are asked to compute the distance between pattern and the text at every…

Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…