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Suffix Tree
[chapter]
2017
Encyclopedia of Database Systems
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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]
2004
Handbook of Data Structures and Applications
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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?
2015
Journal of Discrete Algorithms
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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]
2014
arXiv
pre-print
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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]
2015
Lecture Notes in Computer Science
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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
2012
Theoretical Computer Science
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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
2003
Journal of Discrete Algorithms
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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
2017
Computer journal
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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
2005
Journal of Discrete Algorithms
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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
2018
International Conference on Grammatical Inference
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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
2018
Algorithms
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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]
2014
Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms
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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
2008
Journal of Discrete Algorithms
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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
2004
Journal of Discrete Algorithms
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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
2007
Information Processing Letters
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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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