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http://dx.doi.org/10.6109/jicce.2016.14.1.026

Optimized and Portable FPGA-Based Systolic Cell Architecture for Smith-Waterman-Based DNA Sequence Alignment  

Shah, Hurmat Ali (School of Electrical Engineering, University of Ulsan)
Hasan, Laiq (Department of Computer Systems Engineering, University of Engineering & Technology, Peshawar, Pakistan)
Koo, Insoo (School of Electrical Engineering, University of Ulsan)
Publication Information
Journal of information and communication convergence engineering / v.14, no.1, 2016 , pp. 26-34 More about this Journal
Abstract
The alignment of DNA sequences is one of the important processes in the field of bioinformatics. The Smith-Waterman algorithm (SWA) performs optimally for aligning sequences but is computationally expensive. Field programmable gate array (FPGA) performs the best on parameters such as cost, speed-up, and ease of re-configurability to implement SWA. The performance of FPGA-based SWA is dependent on efficient cell-basic implementation-unit design. In this paper, we present an optimized systolic cell design while avoiding oversimplification, very large-scale integration (VLSI)-level design, and direct mapping of iterative equations such as previous cell designs. The proposed design makes efficient use of hardware resources and provides portability as the proposed design is not based on gate-level details. Our cell design implementing a linear gap penalty resulted in a performance improvement of 32× over a GPP platform and surpassed the hardware utilization of another implementation by a factor of 4.23.
Keywords
Bioinformatics; DNA sequence alignment; FPGA architecture; Smith-Waterman algorithm; Systolic cell;
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