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Nucleic Acid Secondary Structures Prediction with Planar Pseudoknots Using Genetic Algorithm

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Bio-inspired Computing – Theories and Applications (BIC-TA 2016)

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 682))

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Abstract

Nucleic acid nanotechnology offers many methods to fold into a variety of complex and functional nanostructures. These self-assemble scaffolds are valuable in various applications, such as molecular programming, sensing, drug delivery and nanofabrication. However, existing algorithms are typically lacking on predicting pseudoknots structure fast and accurately. This paper proposes a novel genetic algorithm to predict nucleic acid secondary structure including pseudoknots. The length of continues base pairs stacking and free energy are considered to evaluate individuals. Furthermore, the performance of our algorithm is compared with RNAStructure using PseudoBase benchmark instances, and the results show that our algorithm outperforms on accuracy and efficiency.

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Acknowledgment

This work was supported by the National Natural Science Foundation of China (Grant Nos. 61472293, 61502012, 60974112 and 91130034), Natural Science Foundation of Hubei Province (2015CFB335), and the Beijing Natural Science Foundation (4164096).

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Correspondence to He Juanjuan .

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Kai, Z., Shangyi, L., Juanjuan, H., Yunyun, N. (2016). Nucleic Acid Secondary Structures Prediction with Planar Pseudoknots Using Genetic Algorithm. In: Gong, M., Pan, L., Song, T., Zhang, G. (eds) Bio-inspired Computing – Theories and Applications. BIC-TA 2016. Communications in Computer and Information Science, vol 682. Springer, Singapore. https://doi.org/10.1007/978-981-10-3614-9_54

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  • DOI: https://doi.org/10.1007/978-981-10-3614-9_54

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  • Publisher Name: Springer, Singapore

  • Print ISBN: 978-981-10-3613-2

  • Online ISBN: 978-981-10-3614-9

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