The HyperSeq system compares human chromosomes X vs Y using the Smith-Waterman algorithm, the computationally-intensive algorithm for DNA sequence analysis, in under 30 hours. This is a 584-fold speed improvement over the two years required to run this same search on a 64-bit AMD Opteron processor-based PC. A time savings of this magnitude will significantly reduce the computational overhead for many biotechnology researchers, allowing for broader and more thorough investigations. The system provides a turnkey solution for genomic analysis research. Based upon Field Programmable Gate Array (FPGA) technology, the HyperSeq can be customized to suit a variety of algorithms that are computationally or data intensive.