IC-kmedoids: A Clustering Algorithm for RNA Secondary Structure Prediction_Journal of Biomedical Engineering

Authors：

WANGChangwu ,  LIUXiaofeng , WANGBaowen , LIUWenyuan

College of Information Science and Engineering, Yanshan University, Qinhuangdao 066004, China;

Corresponding author：

LIUXiaofeng, Email: liu_xiaofeng6688@163.com

Keywords：

RNA secondary structure; RBP score; clustering algorithm; k-medoids algorithm; incremental candidate set

DOI：

10.7507/1001-5515.20150018

Video：

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Abstract Full text Figures/Tables Video References Cited by

Due to the minimum free energy model, it is very important to predict the RNA secondary structure accurately and efficiently from the suboptimal foldings. Using clustering techniques in analyzing the suboptimal structures could effectively improve the prediction accuracy. An improved k-medoids cluster method is proposed to make this a better accuracy with the RBP score and the incremental candidate set of medoids matrix in this paper. The algorithm optimizes initial medoids through an expanding medoids candidate sets gradually.The predicted results indicated this algorithm could get a higher value of CH and significantly shorten the time for calculating clustering RNA folding structures.

Citation： WANGChangwu, LIUXiaofeng, WANGBaowen, LIUWenyuan. IC-kmedoids: A Clustering Algorithm for RNA Secondary Structure Prediction. Journal of Biomedical Engineering, 2015, 32(1): 99-103. doi: 10.7507/1001-5515.20150018 Copy

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1. TURNER P C. Instant notes in molecular biology[M]. Oxford: BIOS Scientific Publishers Limited, 2000: 360.
2. 王镜岩, 朱圣庚, 徐长法.生物化学[M].第3版.北京:高等教育出版社, 2008:656-659.
3. WOESE C, PACE N. The RNA World[M]. New York: Cold Spring Harbor Laboratory Press, 1993: 91-117.
4. ZUKER M, STIEGLER P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information[J]. Nucleic Acids Res, 1981, 9(1): 133-148.
5. ZUKER M. On finding all suboptimal foldings of an RNA molecule[J]. Science, 1989, 244(4900): 48-52.
6. DING Y, CHAN C Y, LAWRENCE C E. Clustering of RNA secondary structures with application to messenger RNAs[J]. J Mol Biol, 2006, 359(3): 554-571.
7. AGIUS P, BENNETT K P, ZUKER M. Comparing RNA secondary structures using a relaxed base-pair score[J]. RNA, 2010, 16(5): 865-878.
8. CALI AN＇U SKI T, HARABASZ J. A dendrite method for cluster analysis[J]. Comm Statist Theo Meth, 1974, 3(1): 1-27.
9. 夏宁霞, 苏一丹, 覃希.一种高效的K-medoids聚类算法[J].计算机应用研究, 2010, 27(12):4517-4519.
10. PRUITT K D, TATUSOVA T, MAGLOTT D R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins[J]. Nucleic Acids Res, 2007, 35(Database issue): D61-D65.

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