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IPPS
2006
IEEE

MT-ClustalW: multithreading multiple sequence alignment

13 years 9 months ago
MT-ClustalW: multithreading multiple sequence alignment
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 MTClustalW 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.
K. Chaichoompu, Surin Kittitornkun, Sissades Tongs
Added 12 Jun 2010
Updated 12 Jun 2010
Type Conference
Year 2006
Where IPPS
Authors K. Chaichoompu, Surin Kittitornkun, Sissades Tongsima
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