Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures

Publication type:
Journal article
Metadata:
Autoren
Autoren-URL
https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000277447500014&DestLinkType=FullRecord&DestApp=WOS_CPL
DOI
10.1093/bioinformatics/btq135
eISSN
1460-2059
Externe Identifier
  • Clarivate Analytics Document Solution ID: 593IP
  • PubMed Identifier: 20348545
ISSN
1367-4803
Ausgabe der Veröffentlichung
10
Zeitschrift
BIOINFORMATICS
Paginierung
1368 - 1369
Datum der Veröffentlichung
2010
Status
Published
Titel
Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures
Sub types
  • Article
Ausgabe der Zeitschrift
26

Data source: Web of Science (Lite)

Other metadata sources:
Abstract
<jats:title>Abstract</jats:title> <jats:p>Summary: Multiple sequence alignment is an important tool in bioinformatics. Although efficient heuristic algorithms exist for this problem, the exponential growth of biological data demands an even higher throughput. The recent emergence of multi-core technologies has made it possible to achieve a highly improved execution time for many bioinformatics applications. In this article, we introduce an implementation that accelerates the distance matrix computation on x86 and Cell Broadband Engine, a homogeneous and heterogeneous multi-core system, respectively. By taking advantage of multiple processors as well as Single Instruction Multiple Data vectorization, we were able to achieve speed-ups of two orders of magnitude compared to the publicly available implementation utilized in ClustalW.</jats:p> <jats:p>Availability and Implementation: Source codes in C are publicly available at https://sourceforge.net/projects/distmatcomp/</jats:p> <jats:p>Contact:  adri0004@ntu.edu.sg</jats:p>
Autoren
DOI
10.1093/bioinformatics/btq135
eISSN
1367-4811
ISSN
1367-4803
Ausgabe der Veröffentlichung
10
Zeitschrift
Bioinformatics
Sprache
en
Online publication date
2010
Paginierung
1368 - 1369
Datum der Veröffentlichung
2010
Status
Published
Herausgeber
Oxford University Press (OUP)
Herausgeber URL
http://dx.doi.org/10.1093/bioinformatics/btq135
Datum der Datenerfassung
2023
Titel
Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures
Ausgabe der Zeitschrift
26

Data source: Crossref

Abstract
<h4>Summary</h4>Multiple sequence alignment is an important tool in bioinformatics. Although efficient heuristic algorithms exist for this problem, the exponential growth of biological data demands an even higher throughput. The recent emergence of multi-core technologies has made it possible to achieve a highly improved execution time for many bioinformatics applications. In this article, we introduce an implementation that accelerates the distance matrix computation on x86 and Cell Broadband Engine, a homogeneous and heterogeneous multi-core system, respectively. By taking advantage of multiple processors as well as Single Instruction Multiple Data vectorization, we were able to achieve speed-ups of two orders of magnitude compared to the publicly available implementation utilized in ClustalW.<h4>Availability and implementation</h4>Source codes in C are publicly available at https://sourceforge.net/projects/distmatcomp/<h4>Contact</h4>adri0004@ntu.edu.sg
Addresses
  • School of Computer Engineering, Nanyang Technological University, Singapore. adri0004@ntu.edu.sg
Autoren
DOI
10.1093/bioinformatics/btq135
eISSN
1367-4811
Externe Identifier
  • PubMed Identifier: 20348545
Open access
false
ISSN
1367-4803
Ausgabe der Veröffentlichung
10
Zeitschrift
Bioinformatics (Oxford, England)
Schlüsselwörter
  • Sequence Alignment
  • Computational Biology
  • Software
  • Pattern Recognition, Automated
Sprache
eng
Medium
Print-Electronic
Online publication date
2010
Paginierung
1368 - 1369
Datum der Veröffentlichung
2010
Status
Published
Datum der Datenerfassung
2010
Titel
Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures.
Sub types
  • Journal Article
Ausgabe der Zeitschrift
26

Data source: Europe PubMed Central

Abstract
SUMMARY: Multiple sequence alignment is an important tool in bioinformatics. Although efficient heuristic algorithms exist for this problem, the exponential growth of biological data demands an even higher throughput. The recent emergence of multi-core technologies has made it possible to achieve a highly improved execution time for many bioinformatics applications. In this article, we introduce an implementation that accelerates the distance matrix computation on x86 and Cell Broadband Engine, a homogeneous and heterogeneous multi-core system, respectively. By taking advantage of multiple processors as well as Single Instruction Multiple Data vectorization, we were able to achieve speed-ups of two orders of magnitude compared to the publicly available implementation utilized in ClustalW. AVAILABILITY AND IMPLEMENTATION: Source codes in C are publicly available at https://sourceforge.net/projects/distmatcomp/ CONTACT: adri0004@ntu.edu.sg
Autoren
Autoren-URL
https://www.ncbi.nlm.nih.gov/pubmed/20348545
DOI
10.1093/bioinformatics/btq135
eISSN
1367-4811
Ausgabe der Veröffentlichung
10
Zeitschrift
Bioinformatics
Schlüsselwörter
  • Computational Biology
  • Pattern Recognition, Automated
  • Sequence Alignment
  • Software
Sprache
eng
Country
England
Paginierung
1368 - 1369
PII
btq135
Datum der Veröffentlichung
2010
Status
Published
Datum, an dem der Datensatz öffentlich gemacht wurde
2010
Titel
Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures.
Sub types
  • Journal Article
Ausgabe der Zeitschrift
26

Data source: PubMed

Autoren
Zeitschrift
Bioinform.
Artikelnummer
10
Paginierung
1368 - 1369
Datum der Veröffentlichung
2010
Titel
Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures.
Ausgabe der Zeitschrift
26

Data source: DBLP

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