Optimal parallel suffix tree construction
STOC '94 Proceedings of the twenty-sixth annual ACM symposium on Theory of computing
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)
Constructing Suffix Trees On-Line in Linear Time
Proceedings of the IFIP 12th World Computer Congress on Algorithms, Software, Architecture - Information Processing '92, Volume 1 - Volume I
A Database Index to Large Biological Sequences
Proceedings of the 27th International Conference on Very Large Data Bases
Constructing chromosome scale suffix trees
APBC '04 Proceedings of the second conference on Asia-Pacific bioinformatics - Volume 29
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
Linear time algorithms for finding and representing all the tandem repeats in a string
Journal of Computer and System Sciences
Practical methods for constructing suffix trees
The VLDB Journal — The International Journal on Very Large Data Bases
Genome-scale disk-based suffix tree indexing
Proceedings of the 2007 ACM SIGMOD international conference on Management of data
OASIS: an online and accurate technique for local-alignment searches on biological sequences
VLDB '03 Proceedings of the 29th international conference on Very large data bases - Volume 29
Linear pattern matching algorithms
SWAT '73 Proceedings of the 14th Annual Symposium on Switching and Automata Theory (swat 1973)
Serial and parallel methods for i/o efficient suffix tree construction
Proceedings of the 2009 ACM SIGMOD International Conference on Management of data
ERA: efficient serial and parallel suffix tree construction for very long strings
Proceedings of the VLDB Endowment
Efficient parallel construction of suffix trees for genomes larger than main memory
Proceedings of the 20th European MPI Users' Group Meeting
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With advances in sequencing technology and through aggressive sequencing efforts, DNA sequence data sets have been growing at a rapid pace. To gain from these advances, it is important to provide life science researchers with the ability to process and query large sequence data sets. For the past three decades, the suffix tree has served as a fundamental data structure in processing sequential data sets. However, tree construction times on large data sets have been excessive. While parallel suffix tree construction is an obvious solution to reduce execution times, poor locality of reference has limited parallel performance. In this paper, we show that through careful parallel algorithm design, this limitation can be removed, allowing tree construction to scale to massively parallel systems like the IBM Blue Gene. We demonstrate that the entire Human genome can be indexed on 1024 processors in under 15 minutes.