Hardware Accelerated Novel Protein Identification

The proteins in living organisms perform almost every significant function that governs life. A protein's functionality depends upon its physical structure, which depends on its constituent sequence of amino acids as specified by its gene of origin. Advances in mass spectrometry have helped to determine unknown protein sequences but the process is very slow. We review a method of de-novo (novel) protein sequencing that requires a fast search of the genome. In this paper, we present the design of a hardware system that performs this search in a very fast, cost-effective manner. This hardware solution is more than 30 times faster than a similar search in software on a single modem PC, and up to 40 times more cost effective than a computer cluster capable of the same performance. The hardware is FPGA-based to reduce the cost and allow modification of the algorithm, both key requirements of practical protein analysis tools.