SWPS3 - fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2
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Date
2008
Publication Type
Journal Article
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yes
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Abstract
Background. We present swps3, a vectorized implementation of the Smith-Waterman local alignment algorithm optimized for both the Cell/BE and ×86 architectures. The paper describes swps3 and compares its performances with several other implementations. Findings. Our benchmarking results show that swps3 is currently the fastest implementation of a vectorized Smith-Waterman on the Cell/BE, outperforming the only other known implementation by a factor of at least 4: on a Playstation 3, it achieves up to 8.0 billion cell-updates per second (GCUPS). Using the SSE2 instruction set, a quad-core Intel Pentium can reach 15.7 GCUPS. We also show that swps3 on this CPU is faster than a recent GPU implementation. Finally, we note that under some circumstances, alignments are computed at roughly the same speed as BLAST, a heuristic method. Conclusion. The Cell/BE can be a powerful platform to align biological sequences. Besides, the performance gap between exact and heuristic methods has almost disappeared, especially for long protein sequences.
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published
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Volume
1 (107)
Pages / Article No.
1 - 4
Publisher
BioMed Central
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Software
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Subject
BIOLOGISCHE INFORMATIK UND COMPUTERANWENDUNG IN DER BIOLOGIE; SEQUENZVERGLEICH UND SEQUENZHOMOLOGIE (PROTEINE, PEPTIDE); BIOLOGICAL INFORMATICS AND COMPUTER APPLICATIONS IN BIOLOGY; SEQUENCE COMPARISON AND SEQUENCE HOMOLOGY (PROTEINS, PEPTIDES); Query Sequence; Work Thread; Streaming SIMD Extension; Profile Segment; Synergistic Processing Element
Organisational unit
03309 - Gonnet, Gaston (emeritus)
02150 - Dep. Informatik / Dep. of Computer Science