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On-line construction of suffix trees [chapter]

2002 Jewels of Stringology  
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

E. Ukkonen
1995 Algorithmica  
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

Raffaele Giancarlo, Daniela Guaiana
1999 Journal of Complexity  
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]

Shunsuke Inenaga, Masayuki Takeda
2006 Lecture Notes in Computer Science  
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

Martin Senft, Tomáš Dvořák
2012 Journal of Discrete Algorithms  
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

S. Inenaga, H. Hoshino, A. Shinohara, M. Takeda, S. Arikawa
2001 Proceedings Eighth Symposium on String Processing and Information Retrieval  
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

Dimitris Tsirogiannis, Nick Koudas
2010 Proceedings of the 13th International Conference on Extending Database Technology - EDBT '10  
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

Élise Prieur, Thierry Lecroq
2008 Theoretical Computer Science  
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

Marcel H. Schulz, Sebastian Bauer, Peter N. Robinson
2008 International Journal of Bioinformatics Research and Applications  
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

Shunsuke Inenaga, Hiromasa Hoshino, Ayumi Shinohara, Masayuki Takeda, Setsuo Arikawa, Giancarlo Mauri, Giulio Pavesi
2005 Discrete Applied Mathematics  
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]

Matevž Jekovec, Andrej Brodnik
2016 arXiv   pre-print
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]

Shunsuke Inenaga, Hiromasa Hoshino, Ayumi Shinohara, Masayuki Takeda, Setsuo Arikawa, Giancarlo Mauri, Giulio Pavesi
2001 Lecture Notes in Computer Science  
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]

Robert Giegerich, Stefan Kurtz
1994 Lecture Notes in Computer Science  
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

Yanhua Zhang
2012 International Journal of Artificial Intelligence & Applications  
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

J.S. Deogun, Fangrui Ma, Jingyi Yang, A. Benson
2003 36th Annual Hawaii International Conference on System Sciences, 2003. Proceedings of the  
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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