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.
Kai, Zhang; Xinquan, Huang; Xiaolong, Shi; Xiaoli, Qiang; Tao, Song; and Xinzhu, Shi
"A Dynamic Programming Algorithm for Circular Single-stranded DNA Tiles Secondary Structure Prediction,"
Applied Mathematics & Information Sciences: Vol. 07:
6, Article 49.
Available at: https://digitalcommons.aaru.edu.jo/amis/vol07/iss6/49