MT-ClustalW: Multithreading multiple sequence alignment

Chaichoompu, Kridsadakorn; Kittitornkun, Surin; Tongsima, Sissades

doi:10.1109/IPDPS.2006.1639537

MT-ClustalW: Multithreading multiple sequence alignment

Author(s)

Chaichoompu, Kridsadakorn

Kittitornkun, Surin

Tongsima, Sissades

Date Issued

January 1, 2006

Type

Conference Paper

DOI

10.1109/IPDPS.2006.1639537

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 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.

Citation

20th International Parallel and Distributed Processing Symposium IPDPS 2006, 2006, 2006