Results 1  10
of
30,287
More Efficient Algorithms for Closest String and Substring Problems
"... Abstract. The closest string and substring problems find applications in PCR primer design, genetic probe design, motif finding, and antisense drug design. For their importance, the two problems have been extensively studied recently in computational biology. Unfortunately both problems are NPcompl ..."
Abstract

Cited by 17 (2 self)
 Add to MetaCart
(log n). In this paper we provide an O nΣ  O(d) algorithm where Σ is the alphabet. This gives a polynomial time algorithm when d = O(log n) and Σ has constant size. Using the same technique, we additionally provide a more efficient subexponential time algorithm for the closest substring problem
On The Closest String and Substring Problems
 Journal of the ACM
, 2002
"... The problem of finding a center string that is `close' to every given string arises in computational molecular biology and coding theory. This problem has two versions: the Closest String problem and the Closest Substring problem. Given a set of strings S = fs 1 ; s 2 ; : : : ; s n g, each of ..."
Abstract

Cited by 65 (15 self)
 Add to MetaCart
input integer L, asks for the smallest d and a string s, of length L, which is within Hamming distance d away from a substring, of length L, of each s i . This problem is much more elusive than the Closest String problem. The Closest Substring problem is formulated from applications in finding conserved
A Guided Tour to Approximate String Matching
 ACM COMPUTING SURVEYS
, 1999
"... We survey the current techniques to cope with the problem of string matching allowing errors. This is becoming a more and more relevant issue for many fast growing areas such as information retrieval and computational biology. We focus on online searching and mostly on edit distance, explaining t ..."
Abstract

Cited by 584 (38 self)
 Add to MetaCart
We survey the current techniques to cope with the problem of string matching allowing errors. This is becoming a more and more relevant issue for many fast growing areas such as information retrieval and computational biology. We focus on online searching and mostly on edit distance, explaining
The Closest Substring problem with small distances∗
"... In the CLOSEST SUBSTRING problem k strings s1,..., sk are given, and the task is to find a string s of length L such that each string si has a consecutive substring of length L whose distance is at most d from s. The problem is motivated by applications in computational biology. We present two algo ..."
Abstract
 Add to MetaCart
algorithms that can be efficient for small fixed values of d and k: for some functions f and g, the algorithms have running time f (d) ·nO(logd) and g(d,k) ·nO(loglogk), respectively. The second algorithm is based on connections with the extremal combinatorics of hypergraphs. The CLOSEST SUBSTRING problem
CLOSEST SUBSTRING PROBLEMS WITH SMALL DISTANCES∗
"... We study two pattern matching problems that are motivated by applications in computational biology. In the Closest Substring problem k strings s1,..., sk are given, and the task is to find a string s of length L such that each string si has a consecutive substring of length L whose distance is at mo ..."
Abstract
 Add to MetaCart
We study two pattern matching problems that are motivated by applications in computational biology. In the Closest Substring problem k strings s1,..., sk are given, and the task is to find a string s of length L such that each string si has a consecutive substring of length L whose distance
An Efficient Rank Based Approach for Closest String and Closest Substring
, 2011
"... This paper aims to present a new genetic approach that uses rank distance for solving two known NPhard problems, and to compare rank distance with other distance measures for strings. The two NPhard problems we are trying to solve are closest string and closest substring. For each problem we build ..."
Abstract
 Add to MetaCart
This paper aims to present a new genetic approach that uses rank distance for solving two known NPhard problems, and to compare rank distance with other distance measures for strings. The two NPhard problems we are trying to solve are closest string and closest substring. For each problem we
Linear pattern matching algorithms
 IN PROCEEDINGS OF THE 14TH ANNUAL IEEE SYMPOSIUM ON SWITCHING AND AUTOMATA THEORY. IEEE
, 1972
"... In 1970, Knuth, Pratt, and Morris [1] showed how to do basic pattern matching in linear time. Related problems, such as those discussed in [4], have previously been solved by efficient but suboptimal algorithms. In this paper, we introduce an interesting data structure called a bitree. A linear ti ..."
Abstract

Cited by 549 (0 self)
 Add to MetaCart
In 1970, Knuth, Pratt, and Morris [1] showed how to do basic pattern matching in linear time. Related problems, such as those discussed in [4], have previously been solved by efficient but suboptimal algorithms. In this paper, we introduce an interesting data structure called a bitree. A linear
Suffix arrays: A new method for online string searches
, 1991
"... A new and conceptually simple data structure, called a suffix array, for online string searches is introduced in this paper. Constructing and querying suffix arrays is reduced to a sort and search paradigm that employs novel algorithms. The main advantage of suffix arrays over suffix trees is that ..."
Abstract

Cited by 827 (0 self)
 Add to MetaCart
A new and conceptually simple data structure, called a suffix array, for online string searches is introduced in this paper. Constructing and querying suffix arrays is reduced to a sort and search paradigm that employs novel algorithms. The main advantage of suffix arrays over suffix trees
A Closer Look at the Closest String and Closest Substring Problem
"... Let S be a set of k strings over an alphabet Σ; each string has a length between ℓ and n. The Closest Substring Problem (CSSP) is to find a minimal integer d (and a corresponding string t of length ℓ) such that each string s ∈ S has a substring of length ℓ with Hamming distance at most d to t. We sa ..."
Abstract

Cited by 3 (0 self)
 Add to MetaCart
Let S be a set of k strings over an alphabet Σ; each string has a length between ℓ and n. The Closest Substring Problem (CSSP) is to find a minimal integer d (and a corresponding string t of length ℓ) such that each string s ∈ S has a substring of length ℓ with Hamming distance at most d to t. We
Efficient randomized patternmatching algorithms
, 1987
"... We present randomized algorithms to solve the
following stringmatching problem and some of its generalizations: Given a string X of length n (the pattern) and a string Y (the text), find the first occurrence of X as a consecutive block within Y. The algorithms represent strings of length n by much ..."
Abstract

Cited by 397 (1 self)
 Add to MetaCart
We present randomized algorithms to solve the
following stringmatching problem and some of its generalizations: Given a string X of length n (the pattern) and a string Y (the text), find the first occurrence of X as a consecutive block within Y. The algorithms represent strings of length n
Results 1  10
of
30,287