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Accelerating GOR Algorithm Using CUDA |
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PP: 563-567 |
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Author(s) |
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Xinbiao Gan,
Cong liu,
Cong liu,
Zhiying Wang,
Li Shen,
Qi Zhu,
Jie Liu,
Lihua Chi,
Yihui Yan,
Bin Yu,
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Abstract |
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| 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. |
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