MT-ClustalW: Multithreading multiple sequence alignment

DNA sequences; Natural sciences computing; Program processors; Response time (computer systems); Guide tree generation; Multithreaded implementation; Nucleotide sequences; Symmetric Multiprocessor (SMP) machines; Parallel processing systems

Abstract :

[en] ClustalW is the most widely used tool for aligning multiple protein or nucleotide sequences. The alignment is achieved via three stages: pairwise alignment, guide tree generation and progressive alignment. This paper analyzes and enhances a multithreaded implementation of ClustalW called ClustalW-SMP for higher throughput. Our goal is to maximize the degree of parallelism on multithreading ClustalW called MultiThreading-ClustalW (MT-ClustalW). As a result, bioinformatics laboratories are able to use this MT-ClustalW with much less energy consumption on multicore and SMP (Symmetric Multiprocessor) machines than that of PC clusters. The experiment results show that the MT-ClustalW framework can achieve a considerable speedup over the sequential ClustalW and original multithreaded ClustalW-SMP implementations. © 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

Tongsima, S.; National Center for Genetic Engineering and Biotechnology, Klong 1, Klong Luang, Pathumtani 12120, Thailand

Language :

English

Title :

MT-ClustalW: Multithreading multiple sequence alignment

Publication date :

April 2006

Event name :

the 20th International Parallel and Distributed Processing Symposium, 2006 (IPDPS 2006)

Event place :

Rhodes Island, Greece

Event date :

25-04-2006 to 29-04-2006

Audience :

International

Main work title :

the 20th International Parallel and Distributed Processing Symposium, 2006 (IPDPS 2006)

ISBN/EAN :

1-4244-0054-6

Peer reviewed :

Peer reviewed

Commentary :

1424400546; 9781424400546

Available on ORBi :

since 31 January 2014

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