Divide-and-Conquer Algorithm for Clustalw-MPI

Abstract

Multiple sequence alignment continues to be an active field of research in computational biology and the most widely used tool for multiple sequence alignment is ClustalW, which achieves alignment via three steps: pair wise alignment, guide tree generation and progressive alignment. ClustalW-MPI is a parallel implementation of ClustalW. In this paper, a new approach, divide-and-conquer, is implemented which uses ClustalW-MPI for sequence alignment but it gets a better speed up performance than ClustalW-MPI. In this approach, the sequences are first cut down into smaller subsequences by divide-and-conquer technique to minimize the computational space. Then these subsequences are sent to different available processors using message passing interface technique. Those processors align the subsequences by executing ClustalW-MPI simultaneously. After aligning, the results are then sent to the main processor to be concatenated to produce the final alignment. But some quality of the alignment may be compromised in this approach for the introduction of gaps at the start or end of subsequences aligned. Therefore, some heuristic methods for fixing the cut points were suggested for future improvement, such as overlapping alignment and sliding window alignment