A cooperative fast annealing coevolutionary algorithm for protein motif extraction

• Published in: Chinese science bulletin Vol. 52; no. 3; pp. 318 - 323
• Main Authors: Chen, Chao, Tian, YuanXin, Zou, XiaoYong, Cai, PeiXiang, Mo, JinYuan
• Format: Journal Article
• Language: English
• Published: School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, China 01.02.2007
• Subjects: 全局优化; 功能域; 合作法; 快速退火; 蛋白质; 超二级结构; 进化算法; cooperative approach; protein motif; global optimization; evolutionary algorithm; fast annealing
• ISSN: 1001-6538; 1861-9541
• DOI: 10.1007/s11434-007-0047-x

By integrating the cooperative approach with the fast annealing coevolutionary algorithm （FAEA）, a so-called cooperative fast annealing coevolutionary algorithm （CFACA） is presented in this paper for the purpose of solving high-dimensional problems. After the partition of the search space in CFACA, each smaller one is then searched by a separate FAEA. The fitness function is evaluated by combining sub-solutions found by each of the FAEAs. It demonstrates that the CFACA outperforms the FAEA in the domain of function optimization, especially in terms of convergence rate. The current algorithm is also applied to a real optimization problem of protein motif extraction. And a satisfactory result has been obtained with the accuracy of prediction achieving 67.0%, which is in agreement with the result in the PROSITE database.