SWPS3 – fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and ×86/SSE2
<p>Abstract</p> <p>Background</p> <p>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 implementa...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2008-10-01
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| Series: | BMC Research Notes |
| Online Access: | http://www.biomedcentral.com/1756-0500/1/107 |
| _version_ | 1811250348689457152 |
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| author | Krähenbühl Philipp Ledergerber Christian Szalkowski Adam Dessimoz Christophe |
| author_facet | Krähenbühl Philipp Ledergerber Christian Szalkowski Adam Dessimoz Christophe |
| author_sort | Krähenbühl Philipp |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Findings</p> <p>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.</p> <p>Conclusion</p> <p>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.</p> |
| first_indexed | 2024-04-12T16:03:30Z |
| format | Article |
| id | doaj.art-8bb6180acbea49c1add6c38bb5db8bc6 |
| institution | Directory Open Access Journal |
| issn | 1756-0500 |
| language | English |
| last_indexed | 2024-04-12T16:03:30Z |
| publishDate | 2008-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Research Notes |
| spelling | doaj.art-8bb6180acbea49c1add6c38bb5db8bc62022-12-22T03:26:09ZengBMCBMC Research Notes1756-05002008-10-011110710.1186/1756-0500-1-107SWPS3 – fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and ×86/SSE2Krähenbühl PhilippLedergerber ChristianSzalkowski AdamDessimoz Christophe<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Findings</p> <p>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.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1756-0500/1/107 |
| spellingShingle | Krähenbühl Philipp Ledergerber Christian Szalkowski Adam Dessimoz Christophe SWPS3 – fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and ×86/SSE2 BMC Research Notes |
| title | SWPS3 – fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and ×86/SSE2 |
| title_full | SWPS3 – fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and ×86/SSE2 |
| title_fullStr | SWPS3 – fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and ×86/SSE2 |
| title_full_unstemmed | SWPS3 – fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and ×86/SSE2 |
| title_short | SWPS3 – fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and ×86/SSE2 |
| title_sort | swps3 fast multi threaded vectorized smith waterman for ibm cell b e and 86 sse2 |
| url | http://www.biomedcentral.com/1756-0500/1/107 |
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