This paper presents a novel hardware architecture based on Associative Memory technology for sequence alignment. The Associative Memory chip (AMchip) architecture employs a huge amount of parallelization to perform real time combinatorial pattern matching. It can be used to perform very fast searches over a large database using hamming weight as a similarity metric. In the presented hardware platform the AMchip communicates with a Xilinx Zynq ARM CPU + FPGA through high-speed (2.4~Gbps) serial links enabling seamless integration between the software and the hardware acceleration. The result shows that low score sections of a database sequence are eliminated rapidly using this architecture which in turn leads to significant speed up. The outcome of a preliminary study on a selected reference protein database shows that all the matches between query and database sequences found by NCBI-BLAST can be successfully found also by the Associative Memory based algorithm.
['M. Ali Mirzaei', 'Francesco Crescioli', 'Sebastien Viret', 'William Tromeur', 'Giovanni Calderini', 'Giovanni Marchiori', 'G. Baulieu', 'Geoffrey Galbit']
A Novel Associative Memory Based Architecture for Sequence Alignment