Microparallelism and high-performance protein matching
Supercomputing '95 Proceedings of the 1995 ACM/IEEE conference on Supercomputing
Timing for Associative Operations on the MASC Model
IPDPS '01 Proceedings of the 15th International Parallel & Distributed Processing Symposium
Implementation of the Smith-Waterman algorithm on a reconfigurable supercomputing platform
HPRCTA '07 Proceedings of the 1st international workshop on High-performance reconfigurable computing technology and applications: held in conjunction with SC07
Cell-SWat: modeling and scheduling wavefront computations on the cell broadband engine
Proceedings of the 5th conference on Computing frontiers
IPDPS '09 Proceedings of the 2009 IEEE International Symposium on Parallel&Distributed Processing
The new SIMD Implementation of the Smith-Waterman Algorithm on Cell Microprocessor
Fundamenta Informaticae
Journal of Parallel and Distributed Computing
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More sensitive than heuristic methods for searching biological databases, the Smith-Waterman algorithm is widely used but has the drawback of a high quadratic running time. The faster approach extends Smith-Waterman using Associative Massive Parallelism (SWAMP+) for three different parallel architectures: ASsociative Computing (ASC), the ClearSpeed coprocessor, and the Convey Computer FPGA coprocessor. We show that parallel versions of Smith-Waterman can be successfully modified to produce multiple BLAST-like sub-alignments while maintaining the original precision. SWAMP+ combines parallelism and the novel extension producing multiple sub-alignments for pairwise comparisons. Two parallel SWAMP+ implementations for the ASC model and the ClearSpeed CSX-620 use a wavefront approach. Both perform a full traceback in parallel memory, returning multiple sub-alignments. Results show a linear speedup for the 96 processing elements (PEs) on a single ClearSpeed chip. The third SWAMP+ adaptation uses the non-associative Convey Computer FPGA coprocessor. The hybrid system has a Smith-Waterman algorithm suite designed to produce high-speed, high-throughput alignments, optimized for large databases. The Convey Computer Smith-Waterman algorithm suite was extended to produce the additional SWAMP+ sub-alignments efficiently. The parallel sequence alignment algorithms were designed for three different computer systems, all of which contain extensions to produce multiple, additional sub-alignments. This work creates a speedup while providing a deeper exploration of the matched query sequences previously unavailable.