Using PlayStation 3 for Fast Sequence Alignment
Author Information
Author(s): Wirawan Adrianto, Kwoh Chee Keong, Hieu Nim Tri, Schmidt Bertil
Primary Institution: Nanyang Technological University
Hypothesis
Can the PlayStation 3 be used as an efficient computational platform for the Smith-Waterman algorithm?
Conclusion
The PlayStation 3 can serve as a low-cost and efficient computational platform for high-performance sequence alignment applications.
Supporting Evidence
- The implementation achieved a peak performance of 3,646 MCUPS for a query sequence of length 852.
- The PS3 implementation is over 30 times faster than SSEARCH and 1.64 times faster than striped SW.
- The PS3's performance is also three times faster than the CUDA implementation on a single Nvidia GeForce 8800GTX.
Takeaway
The PlayStation 3 can be used to quickly compare DNA or protein sequences, making it a cheaper option for scientists.
Methodology
The study implemented the Smith-Waterman algorithm on the PlayStation 3 using SIMD vectorization and parallel data partitioning.
Limitations
The maximum query sequence length is limited to 852 amino acids due to the 256 KB memory limitation of the SPE local store.
Digital Object Identifier (DOI)
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