Accelerating GOR Algorithm Using CUDA

作者：Gan, Xinbiao^*; Liu, Cong; Wang, Zhiying; Shen, Li; Zhu, Qi; Liu, Jie; Chi, Lihua; Yan, Yihui; Yu, Bin

来源：Applied Mathematics and Information Sciences, 2013, 7(2): 563-567.

DOI：10.12785/amis/072L28

• Protein secondary structure prediction
• GOR
• fine-grained
• onstant cache
• CUDA

Protein secondary structure prediction is very important for its molecular structure. GOR algorithm is one of the most successful computational methods and has been widely used as an efficient analysis tool to predict secondary structure from protein sequence. However, the running time is unbearable with sharp growth in protein database. Fortunately, CUDA (Compute Unified Device Architecture) provides a promising approach to accelerate secondary structure prediction. Therefore, we propose a fine-grained parallel implementation to parallelize GOR-IV package for accelerating protein secondary structure prediction, in which each amino acid would be assigned to one single CUDA thread, hence protein secondary structure prediction would be parallelized by many CUDA threads simultaneously, and constant cache is resorted to cache parameter table. Experimental results show a speedup factor is more than 173X over original GOR-IV version.

• 出版日期2013-6
• 单位武汉大学; 中国人民解放军国防科学技术大学