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From Ukkonen to McCreight and Weiner: A Unifying View of LinearTime Suffix Tree Constructions
 ALGORITHMICA
, 1997
"... We review the linear time suffix tree constructions by Weiner, McCreight, and Ukkonen. We use the terminology of the most recent algorithm, Ukkonen's online construction, to explain its historic predecessors. This reveals relationships much closer than one would expect, since the three algorith ..."
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Cited by 86 (7 self)
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We review the linear time suffix tree constructions by Weiner, McCreight, and Ukkonen. We use the terminology of the most recent algorithm, Ukkonen's online construction, to explain its historic predecessors. This reveals relationships much closer than one would expect, since the three
OnLine Construction of Suffix Trees
, 1995
"... An online algorithm is presented for constructing the suffix tree for a given string in time linear in the length of the string. The new algorithm has the desirable property of processing the string symbol by symbol from left to right. It has always the suffix tree for the scanned part of the strin ..."
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Cited by 437 (2 self)
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An online algorithm is presented for constructing the suffix tree for a given string in time linear in the length of the string. The new algorithm has the desirable property of processing the string symbol by symbol from left to right. It has always the suffix tree for the scanned part
Lineartime construction of suffix arrays
 In Proc. 14th Symposium on Combinatorial Pattern Matching (CPM ’03
, 2003
"... Abstract. The time complexity of suffix tree construction has been shown to be equivalent to that of sorting: O(n) for a constantsize alphabet or an integer alphabet and O(n logn) for a general alphabet. However, previous algorithms for constructing suffix arrays have the time complexity of O(n l ..."
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Cited by 69 (2 self)
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(n logn) even for a constantsize alphabet. In this paper we present a lineartime algorithm to construct suffix arrays for integer alphabets, which do not use suffix trees as intermediate data structures during its construction. Since the case of a constantsize alphabet can be subsumed
The generalised kTruncated Suffix Tree for timeand spaceefficient searches in multiple DNA or protein sequences
"... Abstract: Efficient searching for specific subsequences in a set of longer sequences is an important component of many bioinformatics algorithms. 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, ..."
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Cited by 4 (2 self)
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, and are thus attractive for a variety of applications. Here, we present an algorithm termed the generalised kTruncated Suffix Tree (kTST), that represents an adaption of Ukkonen’s lineartime suffix tree construction algorithm. The kTST algorithm creates a kdeep tree in linear time that allows rapid searches
Suffix arrays: A new method for online string searches
, 1991
"... A new and conceptually simple data structure, called a suffix array, for online string searches is introduced in this paper. Constructing and querying suffix arrays is reduced to a sort and search paradigm that employs novel algorithms. The main advantage of suffix arrays over suffix trees is that ..."
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Cited by 835 (0 self)
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in some cases slightly better than) suffix trees. The only drawback is that in those instances where the underlying alphabet is finite and small, suffix trees can be constructed in O(N) time in the worst case, versus O(N log N) time for suffix arrays. However, we give an augmented algorithm that
Online lineartime construction of word suffix trees
 in Proc. 17th Ann. Symp. on Combinatorial Pattern Matching (CPM’06
, 2006
"... Abstract. Suffix trees are the key data structure for text string matching, and are used in wide application areas such as bioinformatics and data compression. 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 suffi ..."
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Cited by 7 (1 self)
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application is word and phraselevel search on natural language documents. Andersson et al. proposed an algorithm to build word suffix trees in O(n) expected time with O(k) space. 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
Simple linear work suffix array construction
, 2003
"... Abstract. Suffix trees and suffix arrays are widely used and largely interchangeable index structures on strings and sequences. Practitioners prefer suffix arrays due to their simplicity and space efficiency while theoreticians use suffix trees due to lineartime construction algorithms and more exp ..."
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Cited by 215 (8 self)
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Abstract. Suffix trees and suffix arrays are widely used and largely interchangeable index structures on strings and sequences. Practitioners prefer suffix arrays due to their simplicity and space efficiency while theoreticians use suffix trees due to lineartime construction algorithms and more
Linear pattern matching algorithms
 IN PROCEEDINGS OF THE 14TH ANNUAL IEEE SYMPOSIUM ON SWITCHING AND AUTOMATA THEORY. IEEE
, 1972
"... In 1970, Knuth, Pratt, and Morris [1] showed how to do basic pattern matching in linear time. Related problems, such as those discussed in [4], have previously been solved by efficient but suboptimal algorithms. In this paper, we introduce an interesting data structure called a bitree. A linear ti ..."
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Cited by 546 (0 self)
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time algorithm for obtaining a compacted version of a bitree associated with a given string is presented. With this construction as the basic tool, we indicate how to solve several pattern matching problems, including some from [4], in linear time.
Optimal Suffix Tree Construction with Large Alphabets
, 1997
"... The suffix tree of a string is the fundamental data structure of combinatorial pattern matching. Weiner [Wei73], who introduced the data structure, gave an O(n) time algorithm algorithm for building the suffix tree of an n character string drawn from a constant size alphabet. In the comparison model ..."
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Cited by 151 (0 self)
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was the O(n log n) time comparison based algorithm. We settle this open problem by closing the gap: we build suffix trees in linear time for integer alphabet.
Bidirectional construction of suffix trees
 Nordic Journal of Computing
, 2002
"... Abstract. String matching is critical in information retrieval since in many cases information is stored and manipulated as strings. Constructing and utilizing suitable data structures for text strings, we can solve the string matching problem efficiently. Such structures are called index structures ..."
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Cited by 2 (1 self)
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structures. The suffix tree is certainly the most widelyknown and extensivelystudied structure of this kind. In this paper, we present a lineartime algorithm for bidirectional construction of suffix trees. 1
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