Rapid prototyping of a system-on-a-chip for the BLAST algorithm implementation

In the course of rapid system prototyping of a large scale design and implementation of the BLAST algorithm for bioinformatics, we evaluated two different design methods. First, we used the "traditional" method of design with modeling in C and design and synthesis using VHDL. Second, we used the automated tools MATLAB/Simulink with two different design flows, i.e. the fully automated one from AM TLAB to bitstream, and, the architecture and subsystem development based on the MATLAB/Simulink results. We examine the tradeoffs between designer time, design quality and speed, and resource optimization. We analyze how modern tools such as MATLAB/Simulink can improve architecture design and facilitate "what if" scenarios. We conclude that conventional architecture development and design flow is still required for highly optimized system building but the architecture development capabilities of modern tools need to be assimilated in the design process.