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Issue No. 09 - September (2010 vol. 21)
ISSN: 1045-9219
pp: 1267-1280
Xiandong Meng , Texas A&M University, College Station
Vipin Chaudhary , University at Buffalo, The State University of New York, Buffalo
Advances in bioinformatics research continue to add complexity to the analyses and interpretation of biological data. Certain sequence database searches may take weeks to complete due to complicated data dependencies by dynamic programming. A reconfigurable coprocessor can remove this computational bottleneck and accelerate the operation. This paper presents a heterogeneous computing platform through Message Passing Interface (MPI) enabled enterprise computing infrastructure for high-throughput biological sequence analysis. The computing platform integrates heterogeneous computer architectures including conventional processors with Streaming Single Instruction Multiple Data Extensions 2 (SSE2) instructions, reconfigurable coprocessors, and legacy processors together into one system, and allows each to perform the task to which it is best suited. With appropriate computation and communication scheduling, the integrated heterogeneous computing infrastructure is designed to accommodate various types of accelerators to provide a High-Performance Computing (HPC) framework to support the most widely used life science applications.
Index Term—Heterogeneous computing platform, Smith-Waterman algorithm, dynamic programming, sequence alignment, SIMD, SSE2, FPGA, MPI, HPC.

X. Meng and V. Chaudhary, "A High-Performance Heterogeneous Computing Platform for Biological Sequence Analysis," in IEEE Transactions on Parallel & Distributed Systems, vol. 21, no. , pp. 1267-1280, 2009.
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