Parallel Protein Identification Using an FPGA-Based Solution

The ability to rapidly identify a given protein from small subsamples (i.e. peptides) is at the basis of fundamental applications in the medical field. At the basis of protein identification we have a string matching problem which is computational intensive if we consider that the complexity of the algorithm scales with the length of the string and the number of sweeps of the database that are needed. In this paper we present an improvement for the FPGA-based string matching solution available in the literature improving the amount of parallelism exploited by the solution achieving a 1.63x reduction of the energy needed for the task over the literature and a 5.75x reduction when compared with high-end workstation.