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.

• Type: Conference
• Year: 2006
• Where: IPPS
• Authors: K. Chaichoompu, Surin Kittitornkun, Sissades Tongsima
• Keywords: ClustalW, Clustalw Called Clustalw-smp, Distributed And Parallel Computing, IPPS 2006, Sequential Clustalw