MT-clustalW: multithreading multiple sequence alignment

Authors:
Kridsadakorn Chaichoompu;Surin Kittitornkun;Sissades Tongsima
Affiliations:
Dept. of Computer Engineering, Faculty of Engineering, King Mongkut's Institute of Technology, Thailand;Dept. of Computer Engineering, Faculty of Engineering, King Mongkut's Institute of Technology, Thailand;National Center for Genetic Engineering and Biotechnology, Thailand
Venue:
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
Year:
2006

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Abstract

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.