| The proteins in living organisms perform almost every significant function that governs life. A protein's functionality depends upon its physical structure, which in turn depends on its constituent sequence of amino acids as specified by its gene of origin. While many protein sequences are known, many remain to be discovered. Recent advances in mass spectrometry are capable of determining unknown protein sequences but the process is very slow. We review a new method of de-novo protein sequencing that requires a fast search of the genome. In this thesis, we present the design of FPGA-based hardware that can perform this search in a very fast and cost-effective manner. This hardware solution is between 3 to 60 times more cost effective than an equivalent software platform. In addition, we provide a framework to estimate the cost of the hardware at a desired level of performance. |
