Discrete Binary Adaptive Bat Algorithm for RNA Secondary Structure Prediction

被引：5
|
作者：
Cai, Xingjuan [1 ,2 ]
Li, Wuzhao [1 ,3 ]
Kang, Qi [1 ]
Wang, Lei [1 ]
Wu, Qidi [1 ]
机构：
[1] Tongji Univ, Dept Control Sci & Engn, Shanghai 201804, Peoples R China
[2] Taiyuan Univ Sci & Technol, Complex Syst & Computat Intelligence Lab, Taiyuan 030024, Shanxi, Peoples R China
[3] Jiaxing Vocat Tech Coll, Dept Elect & Mech Engn, Jiaxing 314036, Peoples R China
来源：
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE | 2015年 / 12卷 / 02期
基金：
中国国家自然科学基金;
关键词：
RNA Secondary Structure; Minimum Free Energy; Bat Algorithm;
D O I：
10.1166/jctn.2015.4144
中图分类号：
O6 [化学];
学科分类号：
0703 ;
摘要：
RNA secondary structure is one important problem in bioinformatics. In this paper, one discrete binary adaptive bat algorithm is designed to solve it. In the standard version, pulse rate is exponential increased significantly, and then, pulse rate keeps a constant in most generations, this may result a fix selection pressure. To provide a large selection pressure, a linearly dynamic pulse rate selection strategy is designed. Furthermore, due to the special requirements of RNA secondary structure problem, Sigmoid function is also employed to determine the binary-value of each feature. Ten sequences from the comparative RNA website were selected for the evaluation of the proposed method. Simulation results show adaptive bat algorithm is better than Mfold.
引用
收藏
页码：335 / 339
页数：5
相关论文
共 50 条
  • [1] RNA secondary structure prediction based on binary-coded centroid bat algorithm
    Cao, Yang
    Cui, Zhihua
    [J]. Journal of Bionanoscience, 2014, 8 (05): : 364 - 367
  • [2] Changing Range Bat Algorithm for RNA Secondary Structure Prediction
    Cui, Zhihua
    Cao, Yang
    Li, Feixiang
    Zhu, Zhuanghua
    [J]. JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 2015, 12 (08) : 1968 - 1971
  • [3] A Matrix Algorithm for RNA Secondary Structure Prediction
    Krishnan, S. P. T.
    Khurshid, Mushfique Junayed
    Veeravalli, Bharadwaj
    [J]. PATTERN RECOGNITION IN BIOINFORMATICS, 2010, 6282 : 337 - +
  • [4] RNA Secondary Structure Prediction with Coincidence Algorithm
    Srikamdee, Supawadee
    Wattanapornprom, Warin
    Chongstitvatana, Prabhas
    [J]. 2016 16TH INTERNATIONAL SYMPOSIUM ON COMMUNICATIONS AND INFORMATION TECHNOLOGIES (ISCIT), 2016, : 686 - 690
  • [5] Comparison of permutation-based and binary representation in a genetic algorithm for RNA secondary structure prediction
    Deschênes, A
    Wiese, KC
    Glen, E
    [J]. ADVANCES IN ARTIFICIAL INTELLIGENCE, 2004, 3060 : 549 - 550
  • [6] A Bayesian statistical algorithm for RNA secondary structure prediction
    Ding, Y
    Lawrence, CE
    [J]. COMPUTERS & CHEMISTRY, 1999, 23 (3-4): : 387 - 400
  • [7] A distributed genetic algorithm for RNA secondary structure prediction
    Hendriks, A
    Wiese, KC
    Glen, E
    Deschênes, A
    [J]. CEC: 2003 CONGRESS ON EVOLUTIONARY COMPUTATION, VOLS 1-4, PROCEEDINGS, 2003, : 343 - 350
  • [8] RnaPredict - An evolutionary algorithm for RNA secondary structure prediction
    School of Computing Science, Simon Fraser University, 250-13450 102nd Ave., Surrey, BC V3T 0A3, Canada
    不详
    [J]. IEEE/ACM Trans. Comput. BioL. Bioinf., 2008, 1 (25-41):
  • [9] A special genetic algorithm for RNA secondary structure prediction
    Cui, Qinghua
    Liu, Bing
    Jiang, Tianzi
    Ma, Songde
    [J]. MOLECULAR & CELLULAR PROTEOMICS, 2004, 3 (10) : S315 - S315
  • [10] A statistical sampling algorithm for RNA secondary structure prediction
    Ding, Y
    Lawrence, CE
    [J]. NUCLEIC ACIDS RESEARCH, 2003, 31 (24) : 7280 - 7301
12345