| 基于CUDA的蛋白质翻译后修饰鉴定MS-Alignment算法加速研究* |
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| 引用本文： | 翟艳堂,涂强,郎显宇,陆忠华,迟学斌.基于CUDA的蛋白质翻译后修饰鉴定MS-Alignment算法加速研究*[J].计算机应用研究,2010,27(9):3409-3414. |
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| 作者姓名： | 翟艳堂 涂强 郎显宇 陆忠华 迟学斌 |
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| 作者单位： | 1. 中国科学院,计算机网络信息中心,超级计算中心,北京,100190;中国科学院研究生院,北京,100049
2. 中国科学院,计算机网络信息中心,超级计算中心,北京,100190 |
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| 基金项目： | 中国科学院知识创新工程重大项目基金资助项目(KGGX1-YW-13)；CNIC主任基金资助项目(CNIC_ZR_09005)；财政部国家重大科研装备研制项目(ZDYZ2008-2)；中国科学院院长奖获得者科研专项基金资助 |
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| 摘 要： | 对MS-Alignment算法进行分析得出该算法很难满足大规模数据对鉴定速度的要求，而且具有的一个特点是相同的任务在不同的数据上重复计算，为数据划分提供了基础。基于CUDA编程模型使用图形处理器(GPU)对步骤数据库检索及候选肽段生成进行加速优化，设计了该步骤在单GPU上的实现方法。测试结果表明，此方法平均加速比为30倍以上，效果良好，可以满足蛋白质翻译后修饰鉴定中大规模数据快速计算的需求。
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| 关 键 词： | 蛋白质翻译后修饰鉴定 MS-Alignment 图形处理器 统一计算设备架构 |
Research of CUDA-based acceleration of MS-Alignment for identification of post-translational modifications |
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| ZHAI Yan-tang,TU Qiang,LANG Xian-yu,LU Zhong-hu,CHI Xue-bin.Research of CUDA-based acceleration of MS-Alignment for identification of post-translational modifications[J].Application Research of Computers,2010,27(9):3409-3414. |
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| Authors: | ZHAI Yan-tang TU Qiang LANG Xian-yu LU Zhong-hu CHI Xue-bin |
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| Affiliation: | (1.Supercomputing Center, Computer Network Information Center, Chinese Academy of Science, Beijing 100190, China; 2.Graduate University of Chinese Academy of Science, Beijing 100049, China) |
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| Abstract: | This paper firstly analyzed MS-Alignment. It could not well meet the challenge of large scale data. One of its features was the same computing operations repeat on different data. This feature provided base for data partition. This paper then used GPU (graphics processing units) to accelerate the step of database search and candidate generation. And it presented an optimized method based on CUDA (compute unified device architecture) programming model on single GPU. The experimental results show that the average speedup ratio is more than 30, and the method effectively improves identification speed and is applicable for large scale data requiring for high-speed processing. |
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| Keywords: | identification of post-translational modifications MS-Alignment graphics processing units (GPU) compute unified device architecture (CUDA) |
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