Families of FPGA-based algorithms for approximate string matching

Abstract

Dynamic programming for approximate string matching is a large family of different algorithms, which vary significantly in purpose, complexity, and hardware utilization. Many implementations have been reported, but have typically been point solutions: highly specialized implementations that address only one or a few of the many possible options. We report a set of three component types that address different parts of the DP string matching problem. Multiple, interchangeable implementations are available for each component type. This allows each application to choose the feature set required, then make maximum use of the FPGA fabric according to the resource requirements for that specific application. Synthesis estimates show a 4:1 improvement in time-space performance, according to the options chosen for a specific matching task.