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ERA Revisited: Theoretical and Experimental Evaluation
[article]
2016
arXiv
pre-print
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Efficient construction of the suffix tree given an input text is an active area of research from the time it was first introduced. ...
Both theoretical computer scientists and engineers tackled the problem. In this paper we focus on the fastest practical suffix tree construction algorithm to date, ERA. ...
Therefore, one cannot expect to directly construct the suffix tree using a tree traversal and a single scan of the input string. ...
arXiv:1609.09654v1
fatcat:on6g7keizbeapclcq6tbb656p4
Distributed Splay Suffix Arrays: A New Structure For Distributed String Search
2007
Zenodo
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This data structure combines the features of splay tree and suffix arrays into a new approach which is suitable to implementation on both conventional and clustered computers. ...
But if the string access pattern follows the "90/10" rule, suffix array can not take advantage of the fact that we often find something that we have just found. ...
The complexity will be ( ) O R . c) Use Manber and Myer's string sorting method [7] to finish the construction of suffix array in each node. ...
doi:10.5281/zenodo.1071981
fatcat:aipel2ylvba2pngyzvhujlse2a
Construction of Aho Corasick automaton in linear time for integer alphabets
2006
Information Processing Letters
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A new, efficient implementation of nodes in the Aho Corasick automaton is introduced, which works for suffix trees as well. ...
We present a new simple algorithm that constructs an Aho Corasick automaton for a set of patterns, P , of total length n, in O(n) time and space for integer alphabets. ...
The patterns can be sorted using suffix arrays, by constructing the suffix array for S P , thus sorting all suffixes of S P ; out of these, we can filter only the complete words and receive their sorted ...
doi:10.1016/j.ipl.2005.11.019
fatcat:vjfshafuqbdtvcjv3o7pkwznji
Construction of Aho Corasick Automaton in Linear Time for Integer Alphabets
[chapter]
2005
Lecture Notes in Computer Science
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A new, efficient implementation of nodes in the Aho Corasick automaton is introduced, which works for suffix trees as well. ...
We present a new simple algorithm that constructs an Aho Corasick automaton for a set of patterns, P , of total length n, in O(n) time and space for integer alphabets. ...
The patterns can be sorted using suffix arrays, by constructing the suffix array for S P , thus sorting all suffixes of S P ; out of these, we can filter only the complete words and receive their sorted ...
doi:10.1007/11496656_15
fatcat:kyby4hj5iffnfbku6zyrzzovia
Practical methods for constructing suffix trees
2005
The VLDB journal
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Second, we present a new disk-based suffix tree construction algorithm that is based on a sort-merge paradigm, and show that for constructing very large suffix trees with very little resources, this algorithm ...
Even when the suffix tree fits in memory, it turns out that the processor cache behavior of theoretically optimal suffix tree construction methods is poor, resulting in poor performance. ...
We would like to thank the reviewers of this paper for their careful study of our previous manuscript, and their constructive suggestions. Their comments have helped strengthen this paper. ...
doi:10.1007/s00778-005-0154-8
fatcat:bthtthcevrgqzag7huffc5ckci
Suffix-Sorting via Shannon-Fano-Elias Codes
2010
Algorithms
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Given T , the suffix sorting problem is to construct its suffix array. The direct suffix sorting problem is to construct the suffix array of T directly without using the suffix tree data structure. ...
Some methods for constructing suffix arrays first build the suffix tree, and then construct the suffix array by performing an inorder traversal of the suffix tree. ...
A short version of this paper was presented at the 2008 IEEE Data Compression Conference, Snowbird, Utah. ...
doi:10.3390/a3020145
fatcat:xvxmbjzzm5dbpgoufhqxwqfes4
Subject Index
2005
Journal of Discrete Algorithms
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construction of suf-
fix arrays, 143
Suffix sorting
Space efficient linear time construction of suffix
arrays, 143
Suffix trees
Distributed suffix trees, 176
Tandemly repeated sequences
An exact ...
of minisatellites, 375
Complexity analysis
On the analysis of a simple evolutionary algorithm
on quadratic pseudo-boolean functions, 61
Computational biology
Space efficient linear time construction ...
doi:10.1016/s1570-8667(05)00042-0
fatcat:phytlwupp5hmtddg3ffue5546u
Suffix Sorting via Shannon-Fano-Elias Codes
2008
Data Compression Conference (DCC), Proceedings
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Given T , the suffix sorting problem is to construct its suffix array. The direct suffix sorting problem is to construct the suffix array of T directly without using the suffix tree data structure. ...
Some methods for constructing suffix arrays first build the suffix tree, and then construct the suffix array by performing an inorder traversal of the suffix tree. ...
A short version of this paper was presented at the 2008 IEEE Data Compression Conference, Snowbird, Utah. ...
doi:10.1109/dcc.2008.99
dblp:conf/dcc/AdjerohN08
fatcat:qz2fzhsagfdg3hnpcrba57foqe
Space efficient linear time construction of suffix arrays
2005
Journal of Discrete Algorithms
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Though the suffix tree of a string can be constructed in linear time and the sorted order of suffixes derived from it, a direct algorithm for suffix sorting is of great interest due to the space requirements ...
Our result improves upon the best known direct algorithm for suffix sorting, which takes O(n log n) time. We also show how to construct suffix trees in linear time from our suffix sorting result. ...
It is well known that the suffix tree of a string can be constructed from the sorted order of its suffixes and the lcp array [FM96] . ...
doi:10.1016/j.jda.2004.08.002
fatcat:y7s2hul265berbtc6spjsfy5z4
Simple Linear Work Suffix Array Construction
[chapter]
2003
Lecture Notes in Computer Science
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A suffix array represents the suffixes of a string in sorted order. ...
sort suffixes beginning at positions i mod 3 = 0. 2. sort the remaining suffixes using the information obtained in step one. 3. merge the two sorted sequences obtained in steps one and two. ...
Construct the suffix tree of the remaining suffixes using the result of the first step. 3. Merge the two suffix trees into one. ...
doi:10.1007/3-540-45061-0_73
fatcat:5l6a3kvv5fandemcha7yi4gj6e
Space Efficient Linear Time Construction of Suffix Arrays
[chapter]
2003
Lecture Notes in Computer Science
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Though the suffix tree of a string can be constructed in linear time and the sorted order of suffixes derived from it, a direct algorithm for suffix sorting is of great interest due to the space requirements ...
Our result improves upon the best known direct algorithm for suffix sorting, which takes O(n log n) time. We also show how to construct suffix trees in linear time from our suffix sorting result. ...
It is well known that the suffix tree of a string can be constructed from the sorted order of its suffixes and the lcp array [FM96] . ...
doi:10.1007/3-540-44888-8_15
fatcat:3ij7vh5nsjfbtawz46w5ghgccu
RECONSTRUCTING A SUFFIX ARRAY
2006
International Journal of Foundations of Computer Science
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In this paper we consider the "reconstruction" of a suffix array based on a given reordering of the alphabet, and we describe simple timeand space-efficient algorithms that accomplish it. ...
It thus becomes of interest to study possible alternate orderings of the suffixes in these data structures, that may be easier to construct or more efficient to use. ...
Acknowledgements The research was supported in part by the authors' research grants from the Natural Sciences and Engineering Research Council of Canada. ...
doi:10.1142/s0129054106004418
fatcat:ojmxouxb4zdq3nexwbl6dgprka
Suffix Trees on Words
1999
Algorithmica
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Since traditional suffix tree construction algorithms rely heavily on the fact that all suffixes are inserted, construction of a word suffix tree is nontrivial, in particular when only O(m) construction ...
This word suffix tree represents only the m suffixes that start at word boundaries. These boundaries are determined by delimiters, whose definition depends on the application. ...
Most of the work done on suffix tree construction seems to assume that a suffix tree is implemented as a lexicographic trie. ...
doi:10.1007/pl00009260
fatcat:gdguoegwyvdehotg3rn65xveie
Suffix trees on words
[chapter]
1996
Lecture Notes in Computer Science
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Since traditional suffix tree construction algorithms rely heavily on the fact that all suffixes are inserted, construction of a word suffix tree is nontrivial, in particular when only O(m) construction ...
This word suffix tree represents only the m suffixes that start at word boundaries. These boundaries are determined by delimiters, whose definition depends on the application. ...
Most of the work done on suffix tree construction seems to assume that a suffix tree is implemented as a lexicographic trie. ...
doi:10.1007/3-540-61258-0_9
fatcat:zkqalp6p4rbgjfmbn4hop75u3e
Linear work suffix array construction
2006
Journal of the ACM
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Suffix trees and suffix arrays are widely used and largely interchangeable index structures on strings and sequences. ...
The algorithms for BSP and EREW-PRAM models are asymptotically faster than all previous suffix tree or array construction algorithms. ...
Consequently, the complexity of constructing the suffix tree of a string is the same as the complexity of sorting the characters of the string [19] . ...
doi:10.1145/1217856.1217858
fatcat:icwh6toiwvfqbm3xot6obq4rqa
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