Applied Mathematics & Information Sciences

Author Country (or Countries)

P. R. China


The design of DNA sequences is critical for many research fields such as DNA self-assembly, DNA hybridization arrays, DNA computing, and PCR-based applications. DNA secondary structure prediction is the key part for these DNA nanotechnologies. In this paper, we present a dynamic programming algorithm to predict the secondary structure of single-stranded DNA tiles. The algorithm calculates all possible maximum matches based on the nearest-neighbour model and global energy minimization. Experimental results show that the algorithm performers significantly to predict secondary structures for single-stranded DNA tiles.

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