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ERA Revisited: Theoretical and Experimental Evaluation [article]

Matevž Jekovec, Andrej Brodnik
2016 arXiv   pre-print
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

Tu Kun, Gu Nai-Jie, Bi Kun, Liu Gang, Dong Wan-Li
2007 Zenodo  
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

Shiri Dori, Gad M. Landau
2006 Information Processing Letters  
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]

Shiri Dori, Gad M. Landau
2005 Lecture Notes in Computer Science  
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

Yuanyuan Tian, Sandeep Tata, Richard A. Hankins, Jignesh M. Patel
2005 The VLDB journal  
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

Donald Adjeroh, Fei Nan
2010 Algorithms  
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  
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

Don Adjeroh, Fei Nan
2008 Data Compression Conference (DCC), Proceedings  
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

Pang Ko, Srinivas Aluru
2005 Journal of Discrete Algorithms  
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]

Juha Kärkkäinen, Peter Sanders
2003 Lecture Notes in Computer Science  
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]

Pang Ko, Srinivas Aluru
2003 Lecture Notes in Computer Science  
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

FRANTISEK FRANEK, WILLIAM F. SMYTH
2006 International Journal of Foundations of Computer Science  
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

A. Andersson, N. J. Larsson, K. Swanson
1999 Algorithmica  
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]

Arne Andersson, N. Jesper Larsson, Kurt Swanson
1996 Lecture Notes in Computer Science  
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

Juha Kärkkäinen, Peter Sanders, Stefan Burkhardt
2006 Journal of the ACM  
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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