Suffix arrays: a new method for on-line string searches
SIAM Journal on Computing
Efficient implementation of suffix trees
Software—Practice & Experience
Optimal parallel suffix tree construction
Journal of Computer and System Sciences - Special issue: 26th annual ACM symposium on the theory of computing & STOC'94, May 23–25, 1994, and second annual Europe an conference on computational learning theory (EuroCOLT'95), March 13–15, 1995
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
The grid: blueprint for a new computing infrastructure
The grid: blueprint for a new computing infrastructure
MagPIe: MPI's collective communication operations for clustered wide area systems
Proceedings of the seventh ACM SIGPLAN symposium on Principles and practice of parallel programming
The string B-tree: a new data structure for string search in external memory and its applications
Journal of the ACM (JACM)
Reducing the space requirement of suffix trees
Software—Practice & Experience
Future Generation Computer Systems
A Database Index to Large Biological Sequences
Proceedings of the 27th International Conference on Very Large Data Bases
Distributed Computing in a Heterogeneous Computing Environment
Proceedings of the 5th European PVM/MPI Users' Group Meeting on Recent Advances in Parallel Virtual Machine and Message Passing Interface
Grid enabled MPI solutions for Clusters
CCGRID '03 Proceedings of the 3st International Symposium on Cluster Computing and the Grid
Overcoming the Memory Bottleneck in Suffix Tree Construction
FOCS '98 Proceedings of the 39th Annual Symposium on Foundations of Computer Science
MPICH-G2: a Grid-enabled implementation of the Message Passing Interface
Journal of Parallel and Distributed Computing - Special issue on computational grids
Constructing chromosome scale suffix trees
APBC '04 Proceedings of the second conference on Asia-Pacific bioinformatics - Volume 29
Replacing suffix trees with enhanced suffix arrays
Journal of Discrete Algorithms - SPIRE 2002
An adaptive grid implementation of DNA sequence alignment
Future Generation Computer Systems
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
Practical suffix tree construction
VLDB '04 Proceedings of the Thirtieth international conference on Very large data bases - Volume 30
A cluster-based solution for high performance hmmpfam using EARTH execution model
International Journal of High Performance Computing and Networking
Distributed and paged suffix trees for large genetic databases
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Globus toolkit version 4: software for service-oriented systems
NPC'05 Proceedings of the 2005 IFIP international conference on Network and Parallel Computing
Space and time efficient parallel algorithms and software for EST clustering
IEEE Transactions on Parallel and Distributed Systems
Grid-Enabled BLASTZ: Application to Comparative Genomics
Journal of VLSI Signal Processing Systems
Suffix tree construction algorithms on modern hardware
Proceedings of the 13th International Conference on Extending Database Technology
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The suffix tree is a key data structure for biological sequence analysis, since it permits efficient solutions to many string-based problems. Constructing large suffix trees is challenging because of high memory overheads and poor memory locality. Even though efficient suffix tree construction algorithms exist, their run-time is still very high for long DNA sequences such as whole human chromosomes. In this paper, we are using a hierarchical grid system as a computational platform in order to reduce this run-time significantly. To achieve an efficient mapping onto this type of architecture we introduce a parallel suffix tree construction algorithm that makes use of a new data structure called the common prefix suffix tree. Using this algorithm together with a dynamic load balancing strategy we show that our distributed grid implementation leads to significant run-time savings.