RC-BLAST: Towards a Portable, Cost-Effective Open Source Hardware Implementation
IPDPS '05 Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 7 - Volume 08
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The design of PCR or DNA Chip experiments is a time consuming process where bioinformatics is extensively used. Selecting primers for the DNA chip requires a complex algorithm. Based on several parameters an optimized set of primers is computed for a given gene sequence. This paper describes a parallel architecture that performs the primer selection on a hardware accelerator. This parallel architecture reduces the complexity of the time extensive part from O(n2+m2+mn) to O(1). Compared to software, the parallel architecture gains a speedup of factor 500 using a PCI hardware accelerator. This enables to compute the primers in real-time.