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156
A SpaceEconomical Suffix Tree Construction Algorithm
"... AaSTRXCeV. A new algorithm is presented for constructing auxiliary digital search trees to aid in exactmatch substrlng searching. This algorithm has the same asymptotic running time bound as previously published algorithms, but is more economical in space. Some implementation considerations are di ..."
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AaSTRXCeV. A new algorithm is presented for constructing auxiliary digital search trees to aid in exactmatch substrlng searching. This algorithm has the same asymptotic running time bound as previously published algorithms, but is more economical in space. Some implementation considerations
SpaceEconomical Algorithms for Finding Maximal Unique Matches
 In Proc. 13th Annual Symp. Combinatorial Pattern Matching (CPM
, 2002
"... We show spaceeconomical algorithms for finding maximal unique matches (MUM's) between two strings which are important in large scale genome sequence alignment problems. Our algorithms require only O(n) bits (O(n/log n) words) where n is the total length of the strings. We propose three algorit ..."
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Cited by 14 (2 self)
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We show spaceeconomical algorithms for finding maximal unique matches (MUM's) between two strings which are important in large scale genome sequence alignment problems. Our algorithms require only O(n) bits (O(n/log n) words) where n is the total length of the strings. We propose three
Nordic Journal of Computing BIDIRECTIONAL CONSTRUCTION OF SUFFIX TREES
"... Abstract. String matching is critical in information retrieval since in many cases information is stored and manipulated as strings. Constructing and utilizing a suitable data structure for a text string, we can solve the string matching problem efficiently. Such a structure is called an index struc ..."
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structure. Suffix trees are certainly the most widelyknown and extensivelystudied structure of this kind. In this paper, we present a lineartime algorithm for bidirectional construction of suffix trees. The algorithm proposed is also applicable to bidirectional construction of directed acyclic word
The average profile of suffix trees
 In The Fourth Workshop on Analytic Algorithmics and Combinatorics
, 2007
"... The internal profile of a tree structure denotes the number of internal nodes found at a specific level of the tree. Similarly, the external profile denotes the number of leaves on a level. The profile is of great interest because of its intimate connection to many other parameters of trees. For ins ..."
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Cited by 1 (1 self)
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. For instance, the depth, fillup level, height, path length, shortest path, and size of trees can each be interpreted in terms of the profile. The current study is motivated by the work of Park et al. [22], which was a comprehensive study of the profile of tries constructed from independent strings (also, each
Impact of Buffering on Persistent Suffix Tree Construction
"... Suffix trees are indexes that are used commonly to solve many pattern search and discovery problems in an efficient manner over relatively static text. They are considered a powerful datastructure for various sequence processing tasks in the bioinformatics domain. A serious disadvantage of suffix t ..."
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by standard suffix tree construction algorithms. In this paper, using a variety of DNA sequences as our testbed, we empirically evaluate two practical issues not considered before, that impact the persistent online construction of suffix trees. First, the impact of buffering – in terms of policies
Engineering a lightweight suffix array construction algorithm (Extended Abstract)
"... In this paper we consider the problem of computing the suffix array of a text T [1, n]. This problem consists in sorting the suffixes of T in lexicographic order. The suffix array [16] (or pat array [9]) is a simple, easy to code, and elegant data structure used for several fundamental string matchi ..."
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Cited by 81 (3 self)
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to user queries in websearch engines [22]. In all these applications the construction of the suffix array is the computational bottleneck both in time and space. This motivated our interest in designing yet another suffix array construction algorithm which is fast and "lightweight" in the sense
Dynamic Extended Suffix Arrays
, 2009
"... The suffix tree data structure has been intensively described, studied and used in the eighties and nineties, its lineartime construction counterbalancing his spaceconsuming requirements. An equivalent data structure, the suffix array, has been described by Manber and Myers in 1990. This spaceeco ..."
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Cited by 9 (2 self)
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The suffix tree data structure has been intensively described, studied and used in the eighties and nineties, its lineartime construction counterbalancing his spaceconsuming requirements. An equivalent data structure, the suffix array, has been described by Manber and Myers in 1990. This spaceeconomical
Suffix Array of Alignment: A Practical Index for Similar Data
"... Abstract. The suffix tree of alignment is an index data structure for similar strings. Given an alignment of similar strings, it stores all suffixes of the alignment, called alignmentsuffixes. An alignmentsuffix represents one suffix of a string or suffixes of multiple strings starting at the sa ..."
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Cited by 2 (2 self)
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spaceeconomical version of the suffix tree of alignment, named the suffix array of alignment (SAA). Given an alignment of similar strings, the SAA for is a lexicographically sorted list of all the alignmentsuffixes of . The SAA supports pattern search as efficiently as the generalized suffix array
Online Construction of compact suffix vectors and maximal repeats ∗
"... A suffix vector of a string is an index data structure equivalent to a suffix tree. It was first introduced by Monostori et al. in 2001 [9, 10, 11]. They proposed a linear construction algorithm of an extended suffix vector then another linear algorithm to transform an extended suffix vector into a ..."
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more space economical compact suffix vector. We propose an online linear algorithm for directly constructing a compact suffix vector. Not only we show that it is possible to directly build a compact suffix vector but we will also show that this online construction can be faster than the construction
ClosestPoint Problems in Computational Geometry
, 1997
"... This is the preliminary version of a chapter that will appear in the Handbook on Computational Geometry, edited by J.R. Sack and J. Urrutia. A comprehensive overview is given of algorithms and data structures for proximity problems on point sets in IR D . In particular, the closest pair problem, th ..."
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Cited by 73 (14 self)
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, the exact and approximate postoffice problem, and the problem of constructing spanners are discussed in detail. Contents 1 Introduction 1 2 The static closest pair problem 4 2.1 Preliminary remarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 2.2 Algorithms that are optimal in the algebraic
Results 1  10
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