An FPGA implementation of multiple sequence alignment based on Carrillo-Lipman method

Multiple Sequence alignment problems in computational biology have been focused recently because of the rapid growth ofsequencedatabases. B computing alia iment. we can understand similarity among, (lie sequences. It) this paper. we describe a compact system with an FPGA board and a host computer for multiple sequence alignment based oil Carrillo-Lipman method. It our system, two dimensional dynamic programming is repeatedly applied along other dimensions to realize multidimensional search with a simple and common architecture, and unnecessary parts of the search space for finding the optimal alignment are skipped using Carrillo-Lipman method to reduce the computation time.