FPGA based architecture for DNA sequence comparison and database search

DNA sequence comparison is a computationally intensive problem, known widely since the competition for human DNA decryption. Database search for DNA sequence comparison is of great value to computational biologists. Several algorithms have been developed and implemented to solve this problem efficiently, but from a user base point of view the BLAST algorithm is the most widely used one. In this paper, we present a new architecture for the BLAST algorithm. The new architecture was fully designed, placed and routed. The post place-and-route cycle-accurate simulation, accounting for the I/O, shows a better performance than a cluster of workstations running highly optimized code over identical datasets. The new architecture and detailed performance results are presented in this paper