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A fast bitvector algorithm for approximate string matching based on dynamic programming
 J. ACM
, 1999
"... Abstract. The approximate string matching problem is to find all locations at which a query of length m matches a substring of a text of length n with korfewer differences. Simple and practical bitvector algorithms have been designed for this problem, most notably the one used in agrep. These alg ..."
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Cited by 190 (2 self)
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Abstract. The approximate string matching problem is to find all locations at which a query of length m matches a substring of a text of length n with korfewer differences. Simple and practical bitvector algorithms have been designed for this problem, most notably the one used in agrep
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 ..."
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Cited by 584 (38 self)
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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
Fast BitVector Algorithms for Approximate String Matching under Indel Distance
 in Proc. 31st Annual Conference on Current Trends in Theory and Practice of Informatics (SOFSEM 2005), LNCS 3381
"... Abstract. The approximate string matching problem is to find all location at which a query p of length m matches a substring of a text t of length n with at most k differences (insertion, deletion, and substitution). The fastest solutions in practice for this problem are the bitparallel NFA simulat ..."
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Cited by 4 (1 self)
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) are permitted. We also show test results with the algorithms. 1 IndelMYE Algorithm The bitparallel approximate string matching algorithm of Myers [3], MYE, is based on the classical dynamic programming approach where a (m+1) ×(n+1) matrix D is computed using the wellknown recurrence Di,j = min {Di−1,j−1 + δ
Fast Parallel Algorithms for ShortRange Molecular Dynamics
 JOURNAL OF COMPUTATIONAL PHYSICS
, 1995
"... Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of interatomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dyn ..."
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Cited by 622 (6 self)
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Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of interatomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular
A Fast Algorithm for Particle Simulations
, 1987
"... this paper to the case where the potential (or force) at a point is a sum of pairwise An algorithm is presented for the rapid evaluation of the potential and force fields in systems involving large numbers of particles interactions. More specifically, we consider potentials of whose interactions a ..."
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Cited by 1145 (19 self)
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are Coulombic or gravitational in nature. For a the form system of N particles, an amount of work of the order O(N 2 ) has traditionally been required to evaluate all pairwise interactions, un F5F far 1 (F near 1F external ), less some approximation or truncation method is used. The algorithm of the present
Implementation of BitVector Algorithm for Approximate String Matching on Rhodopsin Protein Sequence
"... Approximate string matching has been used in many applications such as, text retrieval, spell checker and DNA sequence matching in computational biology. In this paper, we implemented bitvector algorithm using MATLAB for approximate string matching on Rhodopsin protein sequence of class Aves. Our e ..."
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Approximate string matching has been used in many applications such as, text retrieval, spell checker and DNA sequence matching in computational biology. In this paper, we implemented bitvector algorithm using MATLAB for approximate string matching on Rhodopsin protein sequence of class Aves. Our
A Fast Quantum Mechanical Algorithm for Database Search
 ANNUAL ACM SYMPOSIUM ON THEORY OF COMPUTING
, 1996
"... Imagine a phone directory containing N names arranged in completely random order. In order to find someone's phone number with a probability of , any classical algorithm (whether deterministic or probabilistic)
will need to look at a minimum of names. Quantum mechanical systems can be in a supe ..."
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Cited by 1126 (10 self)
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Imagine a phone directory containing N names arranged in completely random order. In order to find someone's phone number with a probability of , any classical algorithm (whether deterministic or probabilistic)
will need to look at a minimum of names. Quantum mechanical systems can be in a
String theory and noncommutative geometry
 JHEP
, 1999
"... We extend earlier ideas about the appearance of noncommutative geometry in string theory with a nonzero Bfield. We identify a limit in which the entire string dynamics is described by a minimally coupled (supersymmetric) gauge theory on a noncommutative space, and discuss the corrections away from ..."
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Cited by 801 (8 self)
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We extend earlier ideas about the appearance of noncommutative geometry in string theory with a nonzero Bfield. We identify a limit in which the entire string dynamics is described by a minimally coupled (supersymmetric) gauge theory on a noncommutative space, and discuss the corrections away from
Fast Folding and Comparison of RNA Secondary Structures (The Vienna RNA Package)
"... Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and bas ..."
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Cited by 812 (119 self)
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Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions
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 ..."
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Cited by 827 (0 self)
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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
Results 1  10
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