An Optimized System for Multiple Sequence Alignment

Multiple sequence alignment (MSA) is one of the essential operations for identifying functional and structural relations among proteins. The execution of an MSA algorithm requires high-performance platforms. This paper presents a hardware system that speeds up the popular MSA software ClustalW. The proposed design performs the computation of the most time consuming step of the ClustalW. Test results show that the proposed hardware increases the performance of this step up to 85 times.