Multithreaded ClustalW with Improved Optimization for Intel Multi-core Processor

This paper presents the methodology that assists the compiler to optimize ClustalW; the most widely used tool for aligning multiple text-based protein or nucleotide sequences in Bioinformatics. Our goal is to minimize latency and maximize the throughput of execution on multithreading ClustalW called MT-ClustalW: our previous work. As a result, optimized MT-ClustalW is able to fully utilize the machine resources and achieves higher throughput on multicore computers. The experiment results show that our methodology can assist the compiler to optimize the code better than only compiler-optimization and achieve over 2 times faster than the sequential ClustalW. Finally, we analyze the overall result with Amdahl's Law