A time-efficient, linear-space local similarity algorithm
Advances in Applied Mathematics
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
A linear space algorithm for computing maximal common subsequences
Communications of the ACM
Applying scheduling and tuning to on-line parallel tomography
Proceedings of the 2001 ACM/IEEE conference on Supercomputing
Proceedings of the 2001 ACM/IEEE conference on Supercomputing
A hybrid architecture for bioinformatics
Future Generation Computer Systems - Parallel computing technologies (PaCT-2001)
Parallel Biological Sequence Comparison Using Prefix Computations
IPPS '99/SPDP '99 Proceedings of the 13th International Symposium on Parallel Processing and the 10th Symposium on Parallel and Distributed Processing
Massively Parallel Solutions for Molecular Sequence Analysis
IPDPS '02 Proceedings of the 16th International Parallel and Distributed Processing Symposium
Grid enabled MPI solutions for Clusters
CCGRID '03 Proceedings of the 3st International Symposium on Cluster Computing and the Grid
HPCA '99 Proceedings of the 5th International Symposium on High Performance Computer Architecture
Performance analysis of computational biology applications on hierarchical Grid systems
CCGRID '04 Proceedings of the 2004 IEEE International Symposium on Cluster Computing and the Grid
Future Generation Computer Systems - Parallel input/output management techniques (PIOMT) in cluster and grid computing
A minimum cost process in searching for a set of similar DNA sequences
TELE-INFO'06 Proceedings of the 5th WSEAS international conference on Telecommunications and informatics
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In this paper we have described a dynamic programming algorithm to compute k non-intersecting near-optimal alignments in linear space. In order to reduce its runtime significantly, we are using a hierarchical grid system as the computing platform. Static and dynamic load balancing approaches are investigated in order to achieve efficiently mapping onto this type of architecture, which has characteristics such as: (1) the resources in the grid systems have different computational power; (2) the resources usually are connected by networks with widely varying performance characteristics. At last, a new dynamic load balancing approach named scheduler-worker parallel paradigm is proposed and evaluated.