An Approach for Homology Search with Reconfigurable Hardware∗

Smith Waterman Algorithm[1] is an efficient and useful algorithm for homology search problems. However, it can not be processed within reasonable time on desktop computer systems, therefore, dedicated hardware systems which is very expensive are used in general. In this paper, we propose a homology search system with reconfigurable hardware. For reducing the cost, the system is composed of off-the-shelf components. As the result, we could reduce the cost to thousands of dollars and achieved 330 times speedup compared with a desktop computer with a 1GHz PentiumIII. The performance is almost comparable with small to middle class dedicated hardware systems.