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DNA
2007
Springer

Hardware Acceleration for Thermodynamic Constrained DNA Code Generation

9 years 11 months ago
Hardware Acceleration for Thermodynamic Constrained DNA Code Generation
Reliable DNA computing requires a large pool of oligonucleotides that do not produce cross-hybridize. In this paper, we present a transformed algorithm to calculate the maximum weight of the 2-stem common subsequence of two DNA oligonucleotides. The result is the key part of the Gibbs free energy of the DNA crosshybridized duplexes based on the nearest-neighbor model. The transformed algorithm preserves the physical data locality and hence is suitable to be implemented using systolic array. A novel hybrid architecture that that consists of a general purpose microprocessor and a hardware accelerator for accelerating the discovery of DNA under thermodynamic constraints is designed, implemented and tested. Experimental results show that the hardware system provides more than 250X speed-up compared to a software only implementation.
Qinru Qiu, Prakash Mukre, Morgan Bishop, Daniel J.
Added 14 Aug 2010
Updated 14 Aug 2010
Type Conference
Year 2007
Where DNA
Authors Qinru Qiu, Prakash Mukre, Morgan Bishop, Daniel J. Burns, Qing Wu
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