MT-ClustalW: multithreading multiple sequence alignment

• Published in: Proceedings 20th IEEE International Parallel & Distributed Processing Symposium p. 8 pp.
• Main Authors: Chaichoompu, K., Kittitornkun, S., Tongsima, S.
• Format: Conference Proceeding Web Resource
• Language: English
• Published: IEEE 2006
• Subjects: Bioinformatics; Biotechnology; Concurrent computing; DNA sequences; Dynamic scheduling; Engineering, computing & technology; Genetic engineering; Guide tree generation; Ingénierie, informatique & technologie; Multithreaded implementation; Multithreading; Natural sciences computing; Nucleotide sequences; Parallel processing; Parallel processing systems; Program processors; Proteins; Response time (computer systems); Symmetric Multiprocessor (SMP) machines; Throughput; Workstations
• ISBN: 1424400546; 9781424400546
• ISSN: 1530-2075
• DOI: 10.1109/IPDPS.2006.1639537

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