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Title:
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ACCURATE PROFILING AND ACCELERATION EVALUATION OF THE SMITH-WATERMAN ALGORITHM USING THE MOLEN PLATFORM |
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Author(s):
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Laiq Hasan , Zaid Al-ars |
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ISBN:
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978-972-8924-56-0 |
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Editors:
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Nuno Guimarães and Pedro Isaías |
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Year:
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2008 |
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Edition:
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Single |
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Keywords:
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Bioinformatics, Sequence Alignment, Smith-Waterman Algorithm, Hardware Accelerators, FPGAs, MOLEN platform |
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Type:
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Full Paper |
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First Page:
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188 |
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Last Page:
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194 |
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Language:
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English |
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Cover:
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Full Contents:
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click to dowload 
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Paper Abstract:
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In this paper, we present an accurate method to evaluate the amount of acceleration gained by the hardware
implementation of the Smith-Waterman algorithm. This is done using the MOLEN Processor Prototype (MOLEN
platform), where algorithms can be executed both as software or as reconfigurable hardware. By profiling the algorithm,
we identify a specific function that consumes 78% of the total runtime. Implementing this function in hardware results in
a speedup of 2.16 in comparison with a software-only implementation. Since the hardware footprint needed for this
implementation is rather small, this speedup is highly efficient in terms of resource utilization. |
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