Gene Matching Using JBits

As the emerging field of bioinformatics continues to expand, the ability to rapidly search large databases of genetic information is becoming increasingly important. Databases containing billions of data elements are routinely compared and searched for matching and near-matching patterns. In this paper we explore the use of run-time reconfiguration using field programmable gate arrays (FPGAs) to provide a compact, high-performance matching solution to accelerate the searching of these genetic databases. This implementation provides approximately an order of magnitude increase in performance while reducing hardware complexity by as much as three orders of magnitude when compared to existing commercial systems.