Accelerator design for protein sequence HMM search
Proceedings of the 20th annual international conference on Supercomputing
Reconfigurable hardware solution to parallel prefix computation
The Journal of Supercomputing
The new SIMD Implementation of the Smith-Waterman Algorithm on Cell Microprocessor
Fundamenta Informaticae
A highly parameterized and efficient FPGA-based skeleton for pairwise biological sequence alignment
IEEE Transactions on Very Large Scale Integration (VLSI) Systems
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Dynamic programming for approximate string matching is a large family of different algorithms, which vary significantly in purpose, complexity, and hardware utilization. Many implementations have reported impressive speed-ups, but have typically been pointsolutions - highly specialized and addressing only one or a few of the many possible options. The problem to be solved is creating a hardware description that implements a broad range of behavioral options without losing efficiency due to feature bloat. We report a set of three component types that address different parts of the DP string matching problem. Multiple, interchangeable implementations are available for each component type. This allows each application to choose the feature set required, then make maximum use of the FPGA fabric according to that application's specific resource requirements. Synthesis estimates show a 4:1 improvement in time-space performance, depending on the options chosen for a specific matching task.