Reconfigurable hardware for molecular biology computing systems

The authors explore the scope of possibilities of the implementation of molecular biology algorithms on a reconfigurable hardware based architecture. In order to demonstrate both the flexibility and power of reconfigurable hardware, two algorithms have been implemented on an architecture constituted by 23 FPGAs (Xilinx XC3090) and 4MB of SRAM. These two algorithms have been chosen because of their biological relevance. One is a classical dynamic programming algorithm that is implemented as a monodimensional systolic array. The other, as described in this paper, is based on pattern detection in long sequences of letters. This algorithm has been implemented as a rapid content addressable memory. It is important to stress the fact that these performances are achieved thanks to the use of the entire possibilities of reconfigurability. This enables one to exploit to the full each level of parallelism of the algorithm. The concept of reconfigurable hardware perfectly suits the needs of molecular biology. The performances demonstrated in this paper are several magnitude orders greater than a 40 MIPS workstation