Hardware accelerator for DNA code word searching

A large and reliable DNA codeword library is key to the success of DNA based computing. Searching for sets of reliable DNA codewords is an NP-hard problem, which can take days on state of art high performance cluster computers. This work presents a hybrid architecture that consists of a general purpose microprocessor and a hardware accelerator for accelerating the multi-deme genetic algorithm (GA) for the application of DNA codeword searching. This work investigates the effect of mating, migration and mutation operators of GA on the performance. The analysis shows that a modified GA without mating and migration is the most effective for DNA codeword searching. The design can be scaled without any penalty on the throughput. As a proof of concept, a hardware accelerator for searching 32base DNA codewords is implemented. Experimental results show that, the hardware implementation is on an average 47000x faster than the software only implementation.