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Multithreaded ClustalW with improved optimization for intel multi-core processor
Chaichoompu, Kridsadakorn; Kittitornkun, S.
2006In the International Symposium on Communications and Information Technologies, 2006 (ISCIT2006)
Peer reviewed
 

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Keywords :
Bioinformatics; Computer networks; Information technology; Nucleic acids; Technology; Telluric prospecting; Throughput; CLUSTALW; Program compilers
Abstract :
[en] This paper presents the methodology that assists the compiler to optimize ClustalW; the most widely used tool for aligning multiple text-based protein or nucleotide sequences in Bioinformatics. Our goal is to minimize latency and maximize the throughput of execution on multithreading ClustalW called MT-ClustalW: our previous work. As a result, Optimized MT-ClustalW is able to fully utilize the machine resources and achieves higher throughput on multicore computers. The experiment results show that our methodology can assist the compiler to optimize the code better than only compiler-optimization and achieve over 2 times faster than the sequential Clustal W. Finally, we analyze the overall result with Amdahl's Law. © 2006 IEEE.
Disciplines :
Engineering, computing & technology: Multidisciplinary, general & others
Author, co-author :
Chaichoompu, Kridsadakorn ;  Université de Liège - ULiège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Bioinformatique
Kittitornkun, S.;  Dept. of Computer Engineering, Faculty of Engineering, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand
Language :
English
Title :
Multithreaded ClustalW with improved optimization for intel multi-core processor
Publication date :
October 2006
Event name :
the International Symposium on Communications and Information Technologies, 2006 (ISCIT2006)
Event place :
Bangkok, Thailand
Event date :
18 October 2006 through 20 October 2006
Audience :
International
Main work title :
the International Symposium on Communications and Information Technologies, 2006 (ISCIT2006)
ISBN/EAN :
0-7803-9741-X
Pages :
590-594
Peer reviewed :
Peer reviewed
Commentary :
73067
Available on ORBi :
since 31 January 2014

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