Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation
2011
Faster Smith-Waterman Database Searches with SIMD Parallelisation
publication
Evidence: high
Author Information
Author(s): Torbjørn Rognes
Primary Institution: Department of Informatics, University of Oslo
Hypothesis
Can further speed be gained in the Smith-Waterman algorithm through new parallelisation approaches?
Conclusion
The new tool SWIPE allows Smith-Waterman database searches to run more than six times faster than previous implementations.
Supporting Evidence
- SWIPE achieved a speed of 106 billion cell updates per second on a dual Intel Xeon X5650 six-core processor system.
- SWIPE was about six times faster than Farrar's previous implementation.
- SWIPE was about twice as fast as BLAST using the BLOSUM50 score matrix.
Takeaway
This study created a new tool that helps compare DNA sequences much faster than before, making it easier to find similarities.
Methodology
The study implemented a new algorithm called SWIPE that processes residues from multiple database sequences in parallel using SIMD technology.
Limitations
The current version of SWIPE cannot search databases larger than about 4 billion amino acids.
Digital Object Identifier (DOI)
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