RNA secondary structure prediction algorithm based on combinatorial optimization algorithm and SVMs method
- Resource Type
- Conference
- Authors
- He, Jing-yuan; Mu, Chao; Huang, Hai-hun
- Source
- Proceedings of the 10th World Congress on Intelligent Control and Automation Intelligent Control and Automation (WCICA), 2012 10th World Congress on. :715-719 Jul, 2012
- Subject
- Bioengineering
Robotics and Control Systems
Signal Processing and Analysis
Components, Circuits, Devices and Systems
Communication, Networking and Broadcast Technologies
Computing and Processing
Prediction algorithms
RNA
Heuristic algorithms
Topology
Classification algorithms
Convergence
Optimization
dynamic neighbor topology
particle optimization algorithm
SVMs
RNA secondary structure prediction
- Language
A new RNA secondary structure prediction algorithm that can predict pseudoknots is proposed, it combines the stem-loop combinatorial optimization algorithm and SVMs(Support Vector Machines, SVMs) method. The algorithm firstly finds out the optimal stem-loop structure and suboptimum structures based on dynamic neighbor topology particle swarm optimization algorithm, and then puts these loops into SVMs. The output from SVMs can decide whether there exist a pseudoknot. The experimental results demonstrate the superiority of our algorithm over the other methods in terms of solution quality and convergence rates.