Study of the RNA Secondary Structure Prediction_Journal of Biomedical Engineering

Authors：

 SUNYing , LUHongwei , GUIJianbin , SONGXuekun

Medical Instrument and Food Engineering College, University of Shanghai for Science and Technology, Shanghai 200093, China;

Corresponding author：

SUNYing, Email: yysyysun@163.com

Keywords：

RNA secondary structure prediction; comparative sequence analysis; minimum free energy; accuracy assessment

DOI：

10.7507/1001-5515.20140200

Video：

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Abstract Full text Figures/Tables Video References Cited by

This paper proposes algorithm in predicting the RNA secondary structure that combines several sequence comparisons, searches the eigenvalue for subsequence division with dynamic programing, utilizing the minimum free energy method. Moreover, the paper assesses the results derived from this new algorithm based on base-pairs distance, climbing distance and morphology distance. The paper also compares the assessment result and the prediction results of different prediction tools, and analyzes the advantages of the new method and its improvement direction.

Citation： SUNYing, LUHongwei, GUIJianbin, SONGXuekun. Study of the RNA Secondary Structure Prediction. Journal of Biomedical Engineering, 2014, 31(5): 1065-1069. doi: 10.7507/1001-5515.20140200 Copy

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8.	ZUKER M. Calculating nucleic acid secondary structure[J]. Curr Opin Struct Biol, 2000, 10(3): 303-310.
9.	MATHEWS D H. Predicting a set of minimal free energy RNA secondary structures common to two sequences[J]. Bioinformatics, 2005, 21(10): 2246-2253.
10.	MOULTON V, ZUKER M, STEEL M, et al. Metrics on RNA secondary structures[J]. J Comput Biol, 2000, 7(1-2): 277-292.
11.	陈翔,卜东波,张法,等.基于局部茎搜索的RNA二级结构预测算法[J].生物化学与生物物理进展,2009,36(1):115-121.
12.	WATTS J M, DANG K K, GORELICK R J, et al. Architecture and secondary structure of an entire HIV-1 RNA genome[J]. Nature, 2009, 460(7256): 711-716.
13.	KACHOURI R, STRIBINSKIS V, ZHU Y, et al. A surprisingly large RNase P RNA in Candida glabrata[J]. RNA, 2005, 11(7): 1064-1072.
14.	TABEI Y, TSUDA K, KIN T, et al. SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments[J]. Bioinformatics, 2006, 22(14): 1723-1729.
15.	骆嘉伟,陈涛.基于茎区组合的RNA二级结构预测算法[J].计算机应用,2010,30(6):1694-1697.

1. 曹国军,邵宁生.RNA 研究相关技术及其应用[J].生命科学,2008,20(2):183-189.
2. SUN Y, YE S H, LU H W. Study of RNA secondary structure prediction algorithms[J]. Advanced Materials Research, 2012, 393-395: 955-960.
3. 邹权,郭茂祖,张涛涛.RNA二级结构预测方法综述[J].电子学报,2008,36(2):331-337.
4. LIU N, WANG T M. A method for rapid similarity analysis of RNA secondary structures[J/OL]. BMC Bioinformatics, 2006, 7: 493. [2012-12-04]. http://www.biomedcentral.com/1471-2105/7/493.
5. 廖波,王天明.RNA二级结构的最小自由能算法[J].生物数学学报,2003,18(3):364-368.
6. HAVGAARD J, KAUR S, GORODKIN J. Comparative ncRNA gene and structure prediction using Foldalign and FoldalignM[J]. Curr Protoc Bioinformatics, 2012, 2012(12): 12.11.1-12.11.15.
7. MATHEWS D H, TURNER D H. Dynalign: an algorithm for finding the secondary structure common to two RNA sequences[J]. J Mol Biol, 2002, 317(2): 191-203.
8. ZUKER M. Calculating nucleic acid secondary structure[J]. Curr Opin Struct Biol, 2000, 10(3): 303-310.
9. MATHEWS D H. Predicting a set of minimal free energy RNA secondary structures common to two sequences[J]. Bioinformatics, 2005, 21(10): 2246-2253.
10. MOULTON V, ZUKER M, STEEL M, et al. Metrics on RNA secondary structures[J]. J Comput Biol, 2000, 7(1-2): 277-292.
11. 陈翔,卜东波,张法,等.基于局部茎搜索的RNA二级结构预测算法[J].生物化学与生物物理进展,2009,36(1):115-121.
12. WATTS J M, DANG K K, GORELICK R J, et al. Architecture and secondary structure of an entire HIV-1 RNA genome[J]. Nature, 2009, 460(7256): 711-716.
13. KACHOURI R, STRIBINSKIS V, ZHU Y, et al. A surprisingly large RNase P RNA in Candida glabrata[J]. RNA, 2005, 11(7): 1064-1072.
14. TABEI Y, TSUDA K, KIN T, et al. SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments[J]. Bioinformatics, 2006, 22(14): 1723-1729.
15. 骆嘉伟,陈涛.基于茎区组合的RNA二级结构预测算法[J].计算机应用,2010,30(6):1694-1697.

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