A Dynamic Programming Algorithm for Circular Single-stranded DNA Tiles Secondary Structure Prediction

Authors

Zhang Kai, School of Computer Science, Wuhan University of Science and Technology, Wuhan 430081, P. R. China \\ Hubei Province Key Laboratory of Intelligent Information Processing and Real-time Industrial System, Wuhan 430081, P. R. ChinaFollow
Huang Xinquan
Shi Xiaolong
Qiang Xiaoli
Song Tao
Shi Xinzhu

Author Country (or Countries)

P. R. China

Abstract

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.

Suggested Reviewers

N/A

Recommended Citation

Kai, Zhang; Xinquan, Huang; Xiaolong, Shi; Xiaoli, Qiang; Tao, Song; and Xinzhu, Shi (2013) "A Dynamic Programming Algorithm for Circular Single-stranded DNA Tiles Secondary Structure Prediction," Applied Mathematics & Information Sciences: Vol. 07: Iss. 6, Article 49.
Available at: https://digitalcommons.aaru.edu.jo/amis/vol07/iss6/49