A study of the partitioned dynamic programming algorithm for genome comparison in FPGA

This paper explores the potential of partitioning the dynamic programming algorithm to utilise the capabilities of FPGA platforms for parallel genome sequence comparison and assembly. We use this to solve the prefix-suffix approximate matching problem to find overlaps between DNA strands in a given sequence. This is achieved by partitioning the basic dynamic programming (DP) algorithm into a series of discrete sub-DP calculations. Analysis of the error rate as a result of this partitioning by applying random sequences as input data is shown, and simulation results confirm good matching with the original algorithm with an error of less that 1.5% in the worst case. Optimisation for array implementation in FPGA is shown and linear scalability for larger arrays is proven. Simulation results of the whole system confirm 98.8% similarity of the overlap adjacent matrix between error and error-free data.