Graphics Card Processing: Acceleration of Multiple Sequence Alignment

ClustalW is the most widely used heuristic method for multiple sequence alignment. It consists of three stages: distance matrix calculation, guide tree compilation, and greedy-fashion alignment. The high computational complexity demands methods to accelerate the algorithm. In this work, the efficient mapping of the progressive alignment stage onto graphics processing unit by using a combination of wavefront and matrix-matrix product techniques will be studied. The experimental results exhibit one order of magnitude speed-up over the serial version.