Abstract
Reliable DNA computing requires a large pool of oligonucleotides that do not 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 cross-hybridized duplexes based on the nearest-neighbor model. The transformed algorithm preserves the physical data locality and hence is suitable for implementation using a systolic array. A novel hybrid architecture 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.
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Qiu, Q., Mukre, P., Bishop, M., Burns, D., Wu, Q. (2008). Hardware Acceleration for Thermodynamic Constrained DNA Code Generation. In: Garzon, M.H., Yan, H. (eds) DNA Computing. DNA 2007. Lecture Notes in Computer Science, vol 4848. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-77962-9_21
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DOI: https://doi.org/10.1007/978-3-540-77962-9_21
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-77961-2
Online ISBN: 978-3-540-77962-9
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