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This paper presents a novel hardware architecture for the Goertzel algorithm used in exon prediction. It also describes the rapid-prototyping methodology for the implementation of this system. The approach used in this work relies on a top-down philosophy which starts from a MATLAB model and ends in a hardware implementation on FPGA. The design was implemented on a PCI FPGA board installed in the PC. The algorithm was implemented in C++ and with Novakod Studio using the parallel synchronous C (psC) language. With this development environment, the design and implementation time of the FPGA module was greatly reduced. The resulting program successfully identified coding regions in DNA sequences.