Research of Biological Sequence Alignment Algorithm and Graphics Hardware Acceleration

This paper is aimed to explore biological sequence alignment method with accuracy,efficiency,low-cost and universality.We achieved dynamic programming algorithms with higher accuracy than the other alignment algorithms,such as lattice diagram algorithm and heuristic algorithm,in computer and mapped it to the graphics hardware by stream model to speed up the algorithm.The alignment time and(million cell updates per second,MCUPS) were used to evaluated the performance of the accelerated algorithm by an example of database alignment scanning.The result showed that the accelerated algorithm greatly improved the alignment speed and ensured the alignment accuracy at the same time.The alignment speed averagely was 18 times and maximally 28 times as fast as that of heuristic algorithm with highest speed at present.