Parallel construction of a suffix tree
14th International Colloquium on Automata, languages and programming
Self-alignments in words and their applications
Journal of Algorithms
Optimal parallel suffix tree construction
STOC '94 Proceedings of the twenty-sixth annual ACM symposium on Theory of computing
Genetic sequence data retrieval and manipulation based on generalized suffix trees
Genetic sequence data retrieval and manipulation based on generalized suffix trees
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
A Space-Economical Suffix Tree Construction Algorithm
Journal of the ACM (JACM)
Making B+- trees cache conscious in main memory
SIGMOD '00 Proceedings of the 2000 ACM SIGMOD international conference on Management of data
Reducing the space requirement of suffix trees
Software—Practice & Experience
On the sorting-complexity of suffix tree construction
Journal of the ACM (JACM)
A Database Index to Large Biological Sequences
Proceedings of the 27th International Conference on Very Large Data Bases
COCOON '96 Proceedings of the Second Annual International Conference on Computing and Combinatorics
Cache Conscious Algorithms for Relational Query Processing
VLDB '94 Proceedings of the 20th International Conference on Very Large Data Bases
A parallel algorithm for the extraction of structured motifs
Proceedings of the 2004 ACM symposium on Applied computing
Engineering a Fast Online Persistent Suffix Tree Construction
ICDE '04 Proceedings of the 20th International Conference on Data Engineering
Constructing Suffix Tree for Gigabyte Sequences with Megabyte Memory
IEEE Transactions on Knowledge and Data Engineering
VLDB '05 Proceedings of the 31st international conference on Very large data bases
Practical methods for constructing suffix trees
The VLDB Journal — The International Journal on Very Large Data Bases
Constructing large suffix trees on a computational grid
Journal of Parallel and Distributed Computing
Genome-scale disk-based suffix tree indexing
Proceedings of the 2007 ACM SIGMOD international conference on Management of data
Adaptive aggregation on chip multiprocessors
VLDB '07 Proceedings of the 33rd international conference on Very large data bases
CellSort: high performance sorting on the cell processor
VLDB '07 Proceedings of the 33rd international conference on Very large data bases
Linear pattern matching algorithms
SWAT '73 Proceedings of the 14th Annual Symposium on Switching and Automata Theory (swat 1973)
A Data Structure for Sponsored Search
ICDE '09 Proceedings of the 2009 IEEE International Conference on Data Engineering
Serial and parallel methods for i/o efficient suffix tree construction
Proceedings of the 2009 ACM SIGMOD International Conference on Management of data
Parallel motif extraction from very long sequences
Proceedings of the 22nd ACM international conference on Conference on information & knowledge management
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Suffix trees are indexing structures that enhance the performance of numerous string processing algorithms. In this paper, we propose cache-conscious suffix tree construction algorithms that are tailored to CMP architectures. The proposed algorithms utilize a novel sample-based cache partitioning algorithm to improve cache performance and exploit on-chip parallelism on CMPs. Furthermore, several compression techniques are applied to effectively trade space for cache performance. Through an extensive experimental evaluation using real text data from different domains, we demonstrate that the algorithms proposed herein exhibit better cache performance than their cache-unaware counterparts and effectively utilize all processing elements, achieving satisfactory speedup.