Strand design for biomolecular computation
Theoretical Computer Science - Natural computing
A weighted insertion-deletion stacked pair thermodynamic metric for DNA codes
DNA'04 Proceedings of the 10th international conference on DNA computing
A stream chip-multiprocessor for bioinformatics
ACM SIGARCH Computer Architecture News
DNA chips for species identification and biological phylogenies
Natural Computing: an international journal
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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.