Transactions on Mass-Data Analysis of Images and Signals P-ISSN1868-6451, E-ISSN 2509-9353
Volume 10 - Number 1 - September 2019 - Page 19-29
The Computing Algorithm of Barrier Tree Based on the Basin Hopping Graph in RNA Structure
Zhendong Liu1,2*, Gang Li2, and Patrick Wang3
1School of Computer Science and Technology, Shandong Jianzhu University Jinan, 250101,China 2Department of Biostatistics, University of California, Los Angeles, Los Angeles, 90095,USA 3College of Computer and Information Science, Northeastern University, Boston, 02115,USA
It is an NP-hard problem for prediction of RNA folding structure including pseudoknots, biostatistics is one method of biological data mining, the computing algorithm of RNA structure data is the important in biology. we investigate the RNA pseudoknotted structure based on characteristics of the RNA folding structure , the paper first introduce the Basin Hopping Graph(BHG) as a novel model of RNA folding landscape. Our paper gives the computing algorithm of barrier tree based on the BHG, the experimental results in Rfam13.0 and PseudoBase indicate that the algorithm is more effective. We have improved several types of pseudoknots in RNA folding structure, and analyze their possible transitions between types of pseudoknots.
Keywords: RNA Folding Structures; Pseudoknots; Algorithm; Basin Hopping Graph
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