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dc.contributor.author
Szalkowski, Adam
dc.contributor.author
Ledergerber, Christian
dc.contributor.author
Krähenbühl, Philipp
dc.contributor.author
Dessimoz, Christophe
dc.date.accessioned
2018-10-31T13:48:41Z
dc.date.available
2018-10-31T13:48:41Z
dc.date.issued
2008
dc.identifier.issn
1756-0500
dc.identifier.other
10.1186/1756-0500-1-107
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/300224
dc.identifier.doi
10.3929/ethz-a-005751921
dc.description.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.
en_US
dc.language.iso
en
en_US
dc.publisher
BioMed Central
dc.rights.uri
http://creativecommons.org/licenses/by/2.0/
dc.subject
BIOLOGISCHE INFORMATIK UND COMPUTERANWENDUNG IN DER BIOLOGIE
en_US
dc.subject
SEQUENZVERGLEICH UND SEQUENZHOMOLOGIE (PROTEINE, PEPTIDE)
en_US
dc.subject
BIOLOGICAL INFORMATICS AND COMPUTER APPLICATIONS IN BIOLOGY
en_US
dc.subject
SEQUENCE COMPARISON AND SEQUENCE HOMOLOGY (PROTEINS, PEPTIDES)
en_US
dc.subject
Query Sequence
en_US
dc.subject
Work Thread
en_US
dc.subject
Streaming SIMD Extension
en_US
dc.subject
Profile Segment
en_US
dc.subject
Synergistic Processing Element
en_US
dc.title
SWPS3 - fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution 2.0 Generic
dc.date.published
2008-10-29
ethz.journal.title
BMC Research Notes
ethz.journal.volume
1
ethz.journal.issue
107
ethz.pages.start
1
ethz.pages.end
4
ethz.version.deposit
publishedVersion
en_US
ethz.code.ddc
5 - Science::570 - Life sciences
en_US
ethz.identifier.nebis
005561181
ethz.publication.place
London
ethz.publication.status
published
en_US
ethz.leitzahl
ETH Zürich::00002 - ETH Zürich::00012 - Lehre und Forschung::00007 - Departemente::02150 - Dep. Informatik / Dep. of Computer Science
en_US
ethz.leitzahl
03309 - Gonnet, Gaston
ethz.leitzahl.certified
03309 - Gonnet, Gaston
ethz.date.deposited
2017-06-08T21:26:25Z
ethz.source
ECOL
ethz.source
ECIT
ethz.identifier.importid
imp59366acda554c58607
ethz.identifier.importid
imp59364c423ad6267237
ethz.ecolpid
eth:41381
ethz.ecitpid
pub:26282
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2018-10-31T13:49:01Z
ethz.rosetta.lastUpdated
2018-10-31T13:49:01Z
ethz.rosetta.versionExported
true
dc.identifier.olduri
http://hdl.handle.net/20.500.11850/150964
dc.identifier.olduri
http://hdl.handle.net/20.500.11850/14623
ethz.COinS
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