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On-line construction of suffix trees
[chapter]
2002
Jewels of Stringology
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An on-line algorithm is presented for constructing the suffix tree for a given string in time linear in the length of the string. ...
Another variation of this method is shown to give in a natural way the well-known algorithms for constructing suffix automata (DAWGs). ...
Kärkkäinen pointed out some inaccuracies in the earlier version [10] of this work. The author is also indebted to E. Sutinen, D. Wood, and, in particular, S. Kurtz and G. A. ...
doi:10.1142/9789812778222_0004
fatcat:dfdvyprl3jarxnqb3hvipfsfie
On-line construction of suffix trees
1995
Algorithmica
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An on-line algorithm is presented for constructing the suffix tree for a given string in time linear in the length of the string. ...
Another variation of this method is shown to give in a natural way the well-known algorithms for constructing suffix automata (DAWGs). ...
Kärkkäinen pointed out some inaccuracies in the earlier version [10] of this work. The author is also indebted to E. Sutinen, D. Wood, and, in particular, S. Kurtz and G. A. ...
doi:10.1007/bf01206331
fatcat:v6ekkbs3wraznfo6s2nto2rlw4
On-line Construction of Two-Dimensional Suffix Trees
1999
Journal of Complexity
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To the best of our knowledge, our technique is the first one that effectively addresses problems related to the on-line construction of two-dimensional suffix trees. ...
For instance, consider the suffix tree of a string x[1, n]. An algorithm building it on-line is such that, when we have read the first i symbols of x[1, n], we have the suffix tree for x[1, i]. ...
Moreover, our gratitude goes to the referees for their competent reviews and most valuable comments that greatly helped the presentation of our ideas. ...
doi:10.1006/jcom.1998.0495
fatcat:zsyvhgxjifgsrnhks5ic6lwr3y
On-Line Linear-Time Construction of Word Suffix Trees
[chapter]
2006
Lecture Notes in Computer Science
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Sparse suffix trees are kind of suffix trees that represent only a subset of suffixes of the input string. In this paper we study word suffix trees, which are one variation of sparse suffix trees. ...
In this paper we present a new word suffix tree construction algorithm with O(n) running time and O(k) space in the worst cases. ...
Ukkonen [18] used suffix links for on-line construction of normal suffix tries. Here we give a new definition of suffix links that is suitable for on-line word suffix trie construction. ...
doi:10.1007/11780441_7
fatcat:oy7q45f2dvbxliakf2vulgy2p4
On-line suffix tree construction with reduced branching
2012
Journal of Discrete Algorithms
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Classical suffix tree construction algorithms by McCreight and Ukkonen spend most of the time looking up the right branch to follow from the current node. ...
of construction time. ...
They are also grateful to the anonymous referees for a number of constructive comments and suggestions that have substantially improved this article. ...
doi:10.1016/j.jda.2012.01.001
fatcat:54txnr4i2vbjtaa6fx2gzdyv34
On-line construction of symmetric compact directed acyclic word graphs
2001
Proceedings Eighth Symposium on String Processing and Information Retrieval
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In this paper, we show an on-line algorithm that constructs an SCDAWG from a given string directly. ...
Blumer et al. gave the first algorithm to construct an SCDAWG from a given string, that works in an off-line manner. ...
The algorithm is based on Ukkonen's on-line suffix tree construction algorithm given in [15] , while the one Crochemore and Vérin gave is based on McCreight's off-line suffix tree construction algorithm ...
doi:10.1109/spire.2001.989743
dblp:conf/spire/InenagaHSTA01
fatcat:kfn5klpzzfbytdpsru4ivlzsna
Suffix tree construction algorithms on modern hardware
2010
Proceedings of the 13th International Conference on Extending Database Technology - EDBT '10
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Suffix trees are indexing structures that enhance the performance of numerous string processing algorithms. ...
In this paper, we propose cache-conscious suffix tree construction algorithms that are tailored to CMP architectures. ...
As we demonstrate in Section 6, the total cost of constructing a suffix tree depends primarily on the time spent on the construction phase. ...
doi:10.1145/1739041.1739075
dblp:conf/edbt/TsirogiannisK10
fatcat:ij42ym6cabf7fng5usnmof5w2y
On-line construction of compact suffix vectors and maximal repeats
2008
Theoretical Computer Science
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We propose an on-line linear algorithm for directly constructing a compact suffix vector. ...
Not only do we show that it is possible to directly build a compact suffix vector but we will also show that this on-line construction can be faster than the construction of the extended suffix vector. ...
The on-line construction of compact suffix vectors is similar to the on-line construction of suffix trees except for the algorithm AddEdge (see Fig. 11 ) called by algorithm BuildSV(y). ...
doi:10.1016/j.tcs.2008.06.017
fatcat:f64iacdfvngffmais4ta5vpb3y
The generalised k-Truncated Suffix Tree for time-and space-efficient searches in multiple DNA or protein sequences
2008
International Journal of Bioinformatics Research and Applications
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Here, we present an algorithm termed the generalised k-Truncated Suffix Tree (kTST), that represents an adaption of Ukkonen's linear-time suffix tree construction algorithm. ...
Generalised suffix trees and suffix arrays allow searches for a pattern of length n in time proportional to n independent of the length of the sequences, and are thus attractive for a variety of applications ...
ADDSTRING(T,s): Add string s to suffix tree T ...
doi:10.1504/ijbra.2008.017165
pmid:18283030
fatcat:7y2hwlsmezadvhdxccctlrdn34
On-line construction of compact directed acyclic word graphs
2005
Discrete Applied Mathematics
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In this work, we present a novel on-line linear-time algorithm that builds the CDAWG for a single string as well as for a set of strings, inspired by Ukkonen's on-line algorithm for constructing suffix ...
An algorithm which directly constructs CDAWGs in linear time and space was first introduced by Crochemore and Vérin, based on McCreight's algorithm for constructing suffix trees. ...
On-line construction of suffix trees This section is devoted to recalling Ukkonen's on-line algorithm to construct suffix trees [34] . ...
doi:10.1016/j.dam.2004.04.012
fatcat:gqpl7dm6wvectgtlhdfviol3zm
ERA Revisited: Theoretical and Experimental Evaluation
[article]
2016
arXiv
pre-print
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In this paper we focus on the fastest practical suffix tree construction algorithm to date, ERA. ...
Efficient construction of the suffix tree given an input text is an active area of research from the time it was first introduced. ...
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
On-Line Construction of Compact Directed Acyclic Word Graphs*
[chapter]
2001
Lecture Notes in Computer Science
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In this work, we present a novel on-line linear-time algorithm that builds the CDAWG for a single string as well as for a set of strings, inspired by Ukkonen's on-line algorithm for constructing suffix ...
An algorithm which directly constructs CDAWGs in linear time and space was first introduced by Crochemore and Vérin, based on McCreight's algorithm for constructing suffix trees. ...
On-Line Construction of Suffix Trees This section is devoted to recalling Ukkonen's on-line algorithm to construct suffix trees [34] . ...
doi:10.1007/3-540-48194-x_16
fatcat:7gbxxcesfjd6zovyspb6mhnpki
Suffix trees in the functioned programming paradigm
[chapter]
1994
Lecture Notes in Computer Science
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Furthermore, we present a new, "lazy" suffix tree construction which is even simpler. We evaluate both imperative and functional implementations of these algorithms. ...
Based on a new terminology of nested suffixes and nested prefixes, we give a simpler and more declarative explanation of these algorithms than was previously known. ...
Ukkonen's on-line Suffix Tree Construction, Functional Version In this section, we review Ukkonen's linear-time on-line suffix tree construction. ...
doi:10.1007/3-540-57880-3_15
fatcat:yxgmvnjrozgnvgzzaydbiuaj3y
Keyword-Driven Suffix Arrays for On-Line Keyword Searching from Documents In Chinese
2012
International Journal of Artificial Intelligence & Applications
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A data structure called Keyword-driven Suffix Array is proposed in this paper for on-line keyword searching from documents in Chinese, based on observation of on-line search pattern and traits of Chinese ...
That is the major bottleneck of suffix Array. ...
Given a keyword K, on-line searching of K from a string S using suffix arrays can break into two phases. One is construction of the suffix array and the other is search. ...
doi:10.5121/ijaia.2012.3503
fatcat:otptiwdk65gfhpwlfd7w2dc7oe
A prototype for multiple whole genome alignment
2003
36th Annual Hawaii International Conference on System Sciences, 2003. Proceedings of the
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To develop our algorithm, we have to solve several problems including decomposition of genomes with a suffix tree, finding an LIS for multiple MUM sequences, and iterative pairwise multiple sequence alignment ...
One of the motivating application is the problem of finding maximum set of conserved regions in closely related microorganisms. * ...
A string of length n has a total of n suffixes, one starting at each position in the string. To construct the suffix tree, we start with a tree consisting of one node as a root. ...
doi:10.1109/hicss.2003.1174803
dblp:conf/hicss/DeogunMYB03
fatcat:n522thc5ynfozms6nu7lspl3be
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