SWPS3 - fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2.
BACKGROUND
We present swps3, a vectorized implementation of the Smith-Waterman local alignment algorithm optimized for both the Cell/BE and x86 architectures. The paper describes swps3 and compares its performances with several other implementations.


RESULTS
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.


CONCLUSIONS
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.
Szalkowski
Adam
A
Department of Computer Science, ETH Zürich, Zurich, Switzerland. adam.szalkowski@inf.ethz.ch
Ledergerber
Christian
C
Krähenbühl
Philipp
P
Dessimoz
Christophe
C