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230
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 suf-fixes of the alignment, called alignment-suffixes. An alignment-suffix rep-resents 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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Abstract. The suffix tree of alignment is an index data structure for similar strings. Given an alignment of similar strings, it stores all suf-fixes of the alignment, called alignment-suffixes. An alignment-suffix rep-resents one suffix of a string or suffixes of multiple strings starting
Dynamic Extended Suffix Arrays
, 2009
"... The suffix tree data structure has been intensively described, studied and used in the eighties and nineties, its linear-time construction counterbalancing his space-consuming requirements. An equivalent data structure, the suffix array, has been described by Manber and Myers in 1990. This space-eco ..."
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Cited by 9 (2 self)
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letter or a factor). This algorithm is based on a recent four-stage algorithm developed for dynamic Burrows-Wheeler Transforms (BWT). For minimizing the space complexity, we are sampling the Suffix Array, a technique used in BWT-based compressed indexes. We furthermore explain how this technique can
Compressed Spaced Suffix Arrays
, 2014
"... Spaced seeds are important tools for similarity search in bioinformatics, and using several seeds together often significantly improves their performance. With existing approaches, however, for each seed we keep a separate linear-size data structure, either a hash table or a spaced suffix array (SSA ..."
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Cited by 1 (1 self)
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Spaced seeds are important tools for similarity search in bioinformatics, and using several seeds together often significantly improves their performance. With existing approaches, however, for each seed we keep a separate linear-size data structure, either a hash table or a spaced suffix array
Succinct suffix arrays based on run-length encoding
- Nordic Journal of Computing
, 2005
"... A succinct full-text self-index is a data structure built on a text T = t1t2...tn, which takes little space (ideally close to that of the compressed text), permits efficient search for the occurrences of a pattern P = p1p2... pm in T, and is able to reproduce any text substring, so the self-index re ..."
Abstract
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Cited by 60 (32 self)
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and some regularities that show up in their suffix arrays and in the Burrows-Wheeler transform of T. This relationship is of independent interest and permits bounding the space occupancy of the RLFM index, as well as that of other existing compressed indexes. Finally, we present some practical
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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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
When indexing equals compression: Experiments with compressing suffix arrays and applications
, 2004
"... We report on a new and improved version of high-order entropy-compressed suffix arrays, which has theoretical performance guarantees similar to those in our earlier work [16], yet represents an improvement in practice. Our experiments indicate that the resulting text index offers state-of-the-art co ..."
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Cited by 46 (5 self)
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We report on a new and improved version of high-order entropy-compressed suffix arrays, which has theoretical performance guarantees similar to those in our earlier work [16], yet represents an improvement in practice. Our experiments indicate that the resulting text index offers state
Robust record linkage blocking using suffix arrays and Bloom filters
- ACM TKDD
"... Record linkage is an important data integration task that has many practical uses for matching, merging and duplicate removal in large and diverse databases. However, a quadratic scalability for the brute force approach necessitates the design of appropriate indexing or blocking techniques. We desig ..."
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Cited by 13 (1 self)
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array method. Efficiently grouping similar suffixes is carried out with the use of a sliding window technique. We carry out an in-depth analysis of our method and show results from experiments using real and synthetic data, which highlights the importance of using efficient indexing and blocking in real
Linearized suffix tree: an efficient . . .
- ALGORITHMICA
, 2008
"... Suffix trees and suffix arrays are fundamental full-text index data struc-tures to solve problems occurring in string processing. Since suffix trees and suffix arrays have different capabilities, some problems are solved more efficiently using suffix trees and others are solved more efficiently us ..."
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are efficient index data struc-tures with the capabilities of both suffix trees and suffix arrays even when the size of an alphabet is large. A linearized suffix tree has all the functionalities of the enhanced suffix array and supports the pattern search in O(m log ||) time. In a different point of view
Generalizations of Suffix Arrays to Multi-Dimensional Matrices
"... We propose multi-dimensional index data structures that generalize suffix arrays to square matrices and cubic matrices. Giancarlo proposed a two-dimensional index data structure, the Lsuffix tree, that generalizes suffix trees to square matrices. However, the construction algorithm for Lsuffix trees ..."
Abstract
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Cited by 3 (0 self)
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We propose multi-dimensional index data structures that generalize suffix arrays to square matrices and cubic matrices. Giancarlo proposed a two-dimensional index data structure, the Lsuffix tree, that generalizes suffix trees to square matrices. However, the construction algorithm for Lsuffix
Abstract An Incomplex Algorithm for Fast Suffix Array Construction
"... Our aim is to provide full text indexing data structures and algorithms for universal usage in text indexing. We present a practical algorithm for suffix array construction. The fundamental algorithm is less complex than other construction algorithms. We achieve very fast construction times for comm ..."
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Our aim is to provide full text indexing data structures and algorithms for universal usage in text indexing. We present a practical algorithm for suffix array construction. The fundamental algorithm is less complex than other construction algorithms. We achieve very fast construction times
Results 1 - 10
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230
