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Suffix Tree [chapter]

Maxime Crochemore, Thierry Lecroq
2017 Encyclopedia of Database Systems  
The same structure arises when minimizing the suffix tree.  ...  SYNONYMS Compact suffix trie DEFINITION The suffix tree S(y) of a non-empty string y of length n is a compact trie representing all the suffixes of the string.  ...  SCIENTIFIC FUNDAMENTALS Suffix trees The suffix tree S(y) of the string y = ababbb ⊔ is presented Figure 2 . It can be seen as a compaction of the suffix trie T (y) of y given Figure 1 .  ... 
doi:10.1007/978-1-4899-7993-3_1142-2 fatcat:4bfq5wt3a5eoxel6hzhzdmsee4

Suffix Trees and Suffix Arrays [chapter]

Srinivas Aluru
2004 Handbook of Data Structures and Applications  
trees and suffix arrays.  ...  This is done by starting with a partial suffix tree for the lexicographically smallest suffix, and repeatedly inserting subsequent suffixes in the suffix array into the tree until the suffix tree is complete  ... 
doi:10.1201/9781420035179.ch29 fatcat:3fjsu4q2cnfjngceepvgij3uvi

A suffix tree or not a suffix tree?

Tatiana Starikovskaya, Hjalte Wedel Vildhøj
2015 Journal of Discrete Algorithms  
In this paper we study the structure of suffix trees. Given an unlabeled tree τ on n nodes and suffix links of its internal nodes, we ask the question "Is τ a suffix tree?"  ...  Such general suffix trees have many applications and are for example needed to allow efficient updates when suffix trees are built online.  ...  See Fig. 1 for an example of a $-suffix tree, a suffix tree, and a tree, which is not a suffix tree. I et al.  ... 
doi:10.1016/j.jda.2015.01.005 fatcat:fkknsewu7veenpjakkl4ixyasm

A Suffix Tree Or Not A Suffix Tree? [article]

Tatiana Starikovskaya, Hjalte Wedel Vildhøj
2014 arXiv   pre-print
In this paper we study the structure of suffix trees. Given an unlabeled tree τ on n nodes and suffix links of its internal nodes, we ask the question "Is τ a suffix tree?"  ...  Such general suffix trees have many applications and are for example needed to allow efficient updates when suffix trees are built online.  ...  Contrary to $-suffix trees, the suffixes in a suffix tree can end in internal non-branching locations of the tree, called implicit suffix nodes.  ... 
arXiv:1403.1364v3 fatcat:imjk6a2kwra33dmrarhqzlfame

A Suffix Tree Or Not a Suffix Tree? [chapter]

Tatiana Starikovskaya, Hjalte Wedel Vildhøj
2015 Lecture Notes in Computer Science  
In this paper we study the structure of suffix trees. Given an unlabeled tree τ on n nodes and suffix links of its internal nodes, we ask the question "Is τ a suffix tree?"  ...  Such general suffix trees have many applications and are for example needed to allow efficient updates when suffix trees are built online.  ...  See Fig. 1 for an example of a $-suffix tree, a suffix tree, and a tree, which is not a suffix tree. I et al.  ... 
doi:10.1007/978-3-319-19315-1_30 fatcat:bnckjfkztnavznoxjmmrmxhgre

On suffix extensions in suffix trees

Dany Breslauer, Giuseppe F. Italiano
2012 Theoretical Computer Science  
In this paper we study the implicit nodes as the suffix tree evolves.  ...  Suffix trees are inherently asymmetric: prefix extensions only cause a few updates, while suffix extensions affect all suffixes causing a wave of updates.  ...  Such suffix trees were called extended suffix trees by Breslauer and Hariharan [8] and implicit suffix trees by Gusfield [22] .  ... 
doi:10.1016/j.tcs.2012.07.018 fatcat:baofbma6jvd65dwrhh2yebkuja

The suffix binary search tree and suffix AVL tree

Robert W. Irving, Lorna Love
2003 Journal of Discrete Algorithms  
The suffix binary search tree (SBST) and its balanced counterpart, the suffix AVL-tree, are conceptually simple, relatively easy to implement, and offer time and space efficiency to rival suffix trees  ...  In the suffix AVL-tree this is O(m + log n) in the worst case. The space requirements are linear in n, generally intermediate between those for a suffix tree and a suffix array.  ...  See also [2] for an indication of suffix tree applications, and [4] for a detailed exposition of suffix trees and suffix arrays.  ... 
doi:10.1016/s1570-8667(03)00034-0 fatcat:4b36d5jzdvfqrmsizzhpwosysa

Relative Suffix Trees

Andrea Farruggia, Travis Gagie, Gonzalo Navarro, Simon J Puglisi, Jouni Sirén
2017 Computer journal  
and fastest compressed suffix trees.  ...  We compress the suffix trees of individual sequences relative to the suffix tree of a reference sequence.  ...  suffix trees (CST).  ... 
doi:10.1093/comjnl/bxx108 pmid:29795706 pmcid:PMC5956352 fatcat:jwabpueiezbr3b6zga7asxyzue

Distributed suffix trees

Raphaël Clifford
2005 Journal of Discrete Algorithms  
We present a new variant of the suffix tree called a distributed suffix tree (DST) which allows for much larger databases of strings to be handled efficiently.  ...  The method is based on a new linear time construction algorithm for subtrees of a suffix tree.  ...  Distributed suffix trees A suffix tree of input string t is a compacted trie of the suffixes of t.  ... 
doi:10.1016/j.jda.2004.08.004 fatcat:6mnw675kerdffejam6ykkqmwc4

Suffix Classification Trees

Wojciech Wieczorek, Olgierd Unold, Lukasz Strak
2018 International Conference on Grammatical Inference  
Suffix Classification Trees The basic data structure which will be used for classification is an SCT (suffix classification tree).  ...  From Suffix Trees to Suffix Classification Trees Let a sample be D + = {x 1 , x 2 , . . . , x r } and D − = {y 1 , y 2 , . . . , y s } for r, s ≥ 1.  ... 
dblp:conf/icgi/WieczorekUS18 fatcat:mjivri5yy5dr3lafyimuth2kfu

Sliding Suffix Tree

Andrej Brodnik, Matevž Jekovec
2018 Algorithms  
We present an indexed version of the sliding window, based on a suffix tree.  ...  We build the sliding suffix tree on top of Ukkonen's online suffix tree construction algorithm in a similar way to Larsson's approach [16] .  ...  Algorithm 1: Query procedure in the sliding suffix tree.  ... 
doi:10.3390/a11080118 fatcat:d7z3b3koxfcnplxxb3apflendm

Wavelet Trees Meet Suffix Trees [chapter]

Maxim Babenko, Pawel Gawrychowski, Tomasz Kociumaka, Tatiana Starikovskaya
2014 Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms  
Next, we switch to stringological context and propose a novel notion of wavelet suffix trees.  ...  In particular, with a wavelet suffix tree we are able to answer in O( |x|) time the following two natural analogues of rank/select queries for suffixes of substrings: for substrings x and y of w count  ...  Puglisi who pointed out that wavelet suffix trees can be useful for BWT-related applications.  ... 
doi:10.1137/1.9781611973730.39 dblp:conf/soda/BabenkoGKS15 fatcat:u5sb6wf4yrg6fmhnr4kp4o5mgm

Converting suffix trees into factor/suffix oracles

Irena Rusu
2008 Journal of Discrete Algorithms  
suffix tree.  ...  A topology-based compression method is defined for (compact) suffix trees. 2.  ...  identical subtrees in a suffix tree (see [6] ).  ... 
doi:10.1016/j.jda.2006.11.005 fatcat:omgg6yeztbac7lymwqf6fc3vqy

Replacing suffix trees with enhanced suffix arrays

Mohamed Ibrahim Abouelhoda, Stefan Kurtz, Enno Ohlebusch
2004 Journal of Discrete Algorithms  
Phase 1: Bucket construction and partial sorting of the suffixes Phase 2: Full sorting of all buckets.  ...  With additional supporting tables, the algorithms used in all these applications run in optimal time and with reduced space consumption compared to the traditional suffix tree data structure.  ...  Suffix Array The suffix array SA is a list including the positions of all lexicographically sorted suffixes of S.  ... 
doi:10.1016/s1570-8667(03)00065-0 fatcat:wr6f2kw2ingu5k6la47v7iw5cy

Computing suffix links for suffix trees and arrays

Moritz G. Maaß
2007 Information Processing Letters  
We present a new and simple algorithm to reconstruct suffix links in suffix trees and suffix arrays. The algorithm is based on observations regarding suffix tree construction algorithms.  ...  With our algorithm we bring suffix arrays even closer to the ease of use and implementation of suffix trees.  ...  Suffix trees and arrays have converged towards each other as a result of the space reduction of suffix trees and the running time enhancement of suffix arrays.  ... 
doi:10.1016/j.ipl.2005.12.012 fatcat:lomrjphapre6vm2squczgxlqcy
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