New indices for text: PAT Trees and PAT arrays
Information retrieval
Replacing suffix trees with enhanced suffix arrays
Journal of Discrete Algorithms - SPIRE 2002
Journal of the ACM (JACM)
Compressed Suffix Arrays and Suffix Trees with Applications to Text Indexing and String Matching
SIAM Journal on Computing
ACM Computing Surveys (CSUR)
Compressed indexes for dynamic text collections
ACM Transactions on Algorithms (TALG)
A taxonomy of suffix array construction algorithms
ACM Computing Surveys (CSUR)
Theoretical Computer Science
Scalable parallel suffix array construction
Parallel Computing
Fast BWT in small space by blockwise suffix sorting
Theoretical Computer Science
Theoretical Computer Science
Dynamic entropy-compressed sequences and full-text indexes
ACM Transactions on Algorithms (TALG)
Better external memory suffix array construction
Journal of Experimental Algorithmics (JEA)
Compressed text indexes: From theory to practice
Journal of Experimental Algorithmics (JEA)
Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections
SPIRE '08 Proceedings of the 15th International Symposium on String Processing and Information Retrieval
Storage and Retrieval of Individual Genomes
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
Breaking a Time-and-Space Barrier in Constructing Full-Text Indices
SIAM Journal on Computing
Dynamic extended suffix arrays
Journal of Discrete Algorithms
Improved dynamic rank-select entropy-bound structures
LATIN'08 Proceedings of the 8th Latin American conference on Theoretical informatics
Dynamic rank-select structures with applications to run-length encoded texts
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
Sampled longest common prefix array
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
Space-efficient construction of Lempel-Ziv compressed text indexes
Information and Computation
Lightweight BWT construction for very large string collections
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
Lightweight data indexing and compression in external memory
LATIN'10 Proceedings of the 9th Latin American conference on Theoretical Informatics
FEMTO: fast search of large sequence collections
CPM'12 Proceedings of the 23rd Annual conference on Combinatorial Pattern Matching
Computing the longest common prefix array based on the Burrows-Wheeler transform
Journal of Discrete Algorithms
Lightweight algorithms for constructing and inverting the BWT of string collections
Theoretical Computer Science
Trends in suffix sorting: a survey of low memory algorithms
ACSC '12 Proceedings of the Thirty-fifth Australasian Computer Science Conference - Volume 122
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We present a fast space-efficient algorithm for constructing compressed suffix arrays (CSA). The algorithm requires O (n logn ) time in the worst case, and only O (n ) bits of extra space in addition to the CSA. As the basic step, we describe an algorithm for merging two CSAs. We show that the construction algorithm can be parallelized in a symmetric multiprocessor system, and discuss the possibility of a distributed implementation. We also describe a parallel implementation of the algorithm, capable of indexing several gigabytes per hour.