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Permuted longest-common-prefix array

by Juha Kärkkäinen, Giovanni Manzini, Simon J. Puglisi - In Proc. 20th CPM, LNCS 5577 , 2009
"... Abstract. The longest-common-prefix (LCP) array is an adjunct to the suffix array that allows many string processing problems to be solved in optimal time and space. Its construction is a bottleneck in practice, taking almost as long as suffix array construction. In this paper, we describe algorithm ..."
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Abstract. The longest-common-prefix (LCP) array is an adjunct to the suffix array that allows many string processing problems to be solved in optimal time and space. Its construction is a bottleneck in practice, taking almost as long as suffix array construction. In this paper, we describe

Sampled Longest Common Prefix Array

by unknown authors
"... Abstract. When augmented with the longest common prefix (LCP) array and some other structures, the suffix array can solve many string processing problems in optimal time and space. A compressed represen-tation of the LCP array is also one of the main building blocks in many compressed suffix tree pr ..."
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Abstract. When augmented with the longest common prefix (LCP) array and some other structures, the suffix array can solve many string processing problems in optimal time and space. A compressed represen-tation of the LCP array is also one of the main building blocks in many compressed suffix tree

Space-time tradeoffs for longest-common-prefix array computation

by Simon J. Puglisi, Andrew Turpin - In Proc. 19th ISAAC , 2008
"... Abstract. The suffix array, a space efficient alternative to the suffix tree, is an important data structure for string processing, enabling efficient and often optimal algorithms for pattern matching, data compression, repeat finding and many problems arising in computational biology. An essential ..."
Abstract - Cited by 8 (1 self) - Add to MetaCart
augmentation to the suffix array for many of these tasks is the Longest Common Prefix (LCP) array. In particular the LCP array allows one to simulate bottom-up and top-down traversals of the suffix tree with significantly less memory overhead (but in the same time bounds). Since 2001 the LCP array has been

Linear-time longest-common-prefix computation in suffix arrays and its applications

by Toru Kasai, Gunho Lee, Hiroki Arimura, Setsuo Arikawa, Kunsoo Park , 2001
"... Abstract. We present a linear-time algorithm to compute the longest common prefix information in suffix arrays. As two applications of our algorithm, we show that our algorithm is crucial to the effective use of block-sorting compression, and we present a linear-time algorithm to simulate the bottom ..."
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Abstract. We present a linear-time algorithm to compute the longest common prefix information in suffix arrays. As two applications of our algorithm, we show that our algorithm is crucial to the effective use of block-sorting compression, and we present a linear-time algorithm to simulate

Suffix Arrays for Structural Strings

by Richard Beal, Don Adjeroh
"... Abstract. The structural match (s-match), originally addressed by the structural suffix tree, helps identify different RNA sequences with the same secondary structure. In this work, we introduce and construct the structural suffix array and structural longest common prefix array, i.e. lightweight su ..."
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Abstract. The structural match (s-match), originally addressed by the structural suffix tree, helps identify different RNA sequences with the same secondary structure. In this work, we introduce and construct the structural suffix array and structural longest common prefix array, i.e. lightweight

Advanced Data Structures Jan-Apr 2012 Lecturer: Venkatesh Raman

by Scribe Esha Ghosh , 2012
"... (Longest Common Prefix) Arrays. In this lecture we will discuss the linear time constructions of these data structures. Recall that, in the Suffix Array, SA[i] = j means that suffix starting at j is the i th in the lexicographic order of all suffixes, and in the LCP array, LCP [i] contains the leng ..."
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(Longest Common Prefix) Arrays. In this lecture we will discuss the linear time constructions of these data structures. Recall that, in the Suffix Array, SA[i] = j means that suffix starting at j is the i th in the lexicographic order of all suffixes, and in the LCP array, LCP [i] contains

Compressed suffix trees for repetitive texts

by Andrés Abeliuk, Gonzalo Navarro - In Proc. 19th SPIRE, LNCS 7608 , 2012
"... Abstract. We design a new compressed suffix tree specifically tailored to highly repetitive text collections. This is particularly useful for sequence analysis on large collections of genomes of the close species. We build on an existing compressed suffix tree that applies statistical compression, a ..."
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, and modify it so that it works on the grammar-compressed version of the longest common prefix array, whose differential version inherits much of the repetitiveness of the text. 1

Longest-Common-Prefix Computation in Burrows-Wheeler Transformed Text

by Ibrahim Umar, Rosni Abdullah , 2006
"... In this paper we consider the existing algorithm for computation of the Longest-Common-Prefix (LCP) array given a text string and its suffix array and adapt it to work on Burrows-Wheeler Transform (BWT) text. We did this by a combination of pre-processing steps and improvement based on existing algo ..."
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In this paper we consider the existing algorithm for computation of the Longest-Common-Prefix (LCP) array given a text string and its suffix array and adapt it to work on Burrows-Wheeler Transform (BWT) text. We did this by a combination of pre-processing steps and improvement based on existing

Translation of Multiword Expressions Using Parallel Suffix Arrays

by Paul Mcnamee, James Mayfield
"... Accurately translating multiword expressions is important to obtain good performance in machine translation, crosslanguage information retrieval, and other multilingual tasks in human language technology. Existing approaches to inducing translation equivalents of multiword units have focused on aggl ..."
Abstract - Cited by 2 (0 self) - Add to MetaCart
introduced by Yamamoto and Church that uses suffix arrays and longest common prefix arrays. Evaluation of the method in multiple language pairs was performed using bilingual lexicons of domainspecific terminology as a gold standard. We found that performance of 50-70%, as measured by mean reciprocal rank

Modifications of the Landau-Vishkin Algorithm Computing Longest Common Extensions via Suffix Arrays and Efficient RMQ computations

by Rodrigo César de Castro Miranda, Mauricio Ayala-Rincón, Leon Solon
"... Approximate string matching is an important problem in Computer Science. The standard solution for this problem is an O(mn) running time and space dynamic programming algorithm for two strings of length m and n. Landau and Vishkin developed an algorithm which uses suffix trees for accelerating the ..."
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common extensions between substrings. We present two O(n) space variations of the Landau and Vishkin algorithm that use range-minimum-queries (RMQ) over the longest common prefix array of an extended suffix array instead of suffix trees for computing the longest common extensions: one which computes
Results 1 - 10 of 97