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Scalable Parallel Suffix Array Construction
"... Abstract. Suffix arrays are a simple and powerful data structure for text processing that can be used for full text indexes, data compression, and many other applications in particular in bioinformatics. We describe the first implementation and experimental evaluation of a scalable parallel algorith ..."
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Cited by 13 (1 self)
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algorithm for suffix array construction. The implementation works on distributed memory computers using MPI, Experiments with up to 128 processors show good constant factors and make it look likely that the algorithm would also scale to considerably larger systems. This makes it possible to build suffix
Faster Lightweight Suffix Array Construction
"... The suffix array is a data structure formed by sorting the suffixes of a string into lexicographical order. It is important for a variety of applications, perhaps most notably pattern matching, pattern discovery and blocksorting data compression. The last decade has seen intensive research toward e ..."
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Cited by 13 (3 self)
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efficient construction of suffix arrays with algorithms striving not only to be fast, but also “lightweight” (in the sense that they use small working memory). In this paper we describe a new lightweight suffix array construction algorithm. By exploiting several interesting properties of suffixes
A taxonomy of suffix array construction algorithms
 ACM Computing Surveys
, 2007
"... In 1990, Manber and Myers proposed suffix arrays as a spacesaving alternative to suffix trees and described the first algorithms for suffix array construction and use. Since that time, and especially in the last few years, suffix array construction algorithms have proliferated in bewildering abunda ..."
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Cited by 76 (12 self)
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In 1990, Manber and Myers proposed suffix arrays as a spacesaving alternative to suffix trees and described the first algorithms for suffix array construction and use. Since that time, and especially in the last few years, suffix array construction algorithms have proliferated in bewildering
An incomplex algorithm for fast suffix array construction
"... The suffix array of a string is a permutation of all starting positions of the string’s suffixes that are lexicographically sorted. We present a practical algorithm for suffix array construction that consists of two easytoimplement components. First it sorts the suffixes with respect to a fixed le ..."
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The suffix array of a string is a permutation of all starting positions of the string’s suffixes that are lexicographically sorted. We present a practical algorithm for suffix array construction that consists of two easytoimplement components. First it sorts the suffixes with respect to a fixed
Simple linear work suffix array construction
, 2003
"... Abstract. Suffix trees and suffix arrays are widely used and largely interchangeable index structures on strings and sequences. Practitioners prefer suffix arrays due to their simplicity and space efficiency while theoreticians use suffix trees due to lineartime construction algorithms and more exp ..."
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Cited by 214 (6 self)
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Abstract. Suffix trees and suffix arrays are widely used and largely interchangeable index structures on strings and sequences. Practitioners prefer suffix arrays due to their simplicity and space efficiency while theoreticians use suffix trees due to lineartime construction algorithms and more
Better external memory suffix array construction
 In: Workshop on Algorithm Engineering & Experiments
, 2005
"... Suffix arrays are a simple and powerful data structure for text processing that can be used for full text indexes, data compression, and many other applications in particular in bioinformatics. However, so far it has looked prohibitive to build suffix arrays for huge inputs that do not fit into main ..."
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Cited by 40 (4 self)
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into main memory. This paper presents design, analysis, implementation, and experimental evaluation of several new and improved algorithms for suffix array construction. The algorithms are asymptotically optimal in the worst case or on the average. Our implementation can construct suffix arrays for inputs
Abstract An Incomplex Algorithm for Fast Suffix Array Construction
"... Our aim is to provide full text indexing data structures and algorithms for universal usage in text indexing. We present a practical algorithm for suffix array construction. The fundamental algorithm is less complex than other construction algorithms. We achieve very fast construction times for comm ..."
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Our aim is to provide full text indexing data structures and algorithms for universal usage in text indexing. We present a practical algorithm for suffix array construction. The fundamental algorithm is less complex than other construction algorithms. We achieve very fast construction times
Abstract Better External Memory Suffix Array Construction
"... Suffix arrays are a simple and powerful data structure for text processing that can be used for full text indexes, data compression, and many other applications in particular in bioinformatics. However, so far it looked prohibitive to build suffix arrays for huge inputs that do not fit into main mem ..."
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memory. This paper presents design, analysis, implementation, and experimental evaluation of several new and improved algorithms for suffix array construction. The algorithms are asymptotically optimal in the worst case or on the average. Our implementation can construct suffix arrays for inputs of up
Fast lightweight suffix array construction and checking
 14th Annual Symposium on Combinatorial Pattern Matching
, 2003
"... We describe an algorithm that, for any v 2 [2; n], constructs the suffix array of a string of length n in O(vn + n log n) time using O(v + n= p v) space in addition to the input (the string) and the output (the suffix array). By setting v = log n, we obtain an O(n log n) time algorithm using O n= p ..."
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Cited by 34 (5 self)
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We describe an algorithm that, for any v 2 [2; n], constructs the suffix array of a string of length n in O(vn + n log n) time using O(v + n= p v) space in addition to the input (the string) and the output (the suffix array). By setting v = log n, we obtain an O(n log n) time algorithm using O n
Parallel suffix array construction by accelerated sampling
"... Abstract. A deterministic BSP algorithm for constructing the suffix array of a given string is presented, based on a technique that we call accelerated sampling. It runs in optimal O(n p) local computation and communication, and requires a near optimal O(log log p) supersteps. The algorithm provides ..."
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Cited by 1 (0 self)
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Abstract. A deterministic BSP algorithm for constructing the suffix array of a given string is presented, based on a technique that we call accelerated sampling. It runs in optimal O(n p) local computation and communication, and requires a near optimal O(log log p) supersteps. The algorithm
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