Using frequency distance filteration for reducing database search workload on GPU-based cloud service

Sheng Ta Lee, Chun Yuan Lin*, Che Lun Hung, Hsuan Ying Huang

*此作品的通信作者

研究成果: Conference contribution同行評審

2 引文 斯高帕斯(Scopus)

摘要

The Smith-Waterman algorithm is the most widely used algorithm to analyze the similarity between protein and DNA sequences and suitable for the database search due to its high sensitivity. However, Smith-Waterman still is a very time-consuming method. CUDA programming can efficiently improve the computations by using the computing power of the massive computing hardware as GPUs. In this paper, we proposed an efficient frequency based filter method instead of just speed up the Smith-Waterman comparison but waste computing resource to deal with those unnecessary comparisons. We implemented the Smith-Waterman algorithm by introduction of the techniques from earlier researches and add in our real-time filter method on Graphic Processing Units to filter unnecessary comparisons. We also design a user friendly interface to provide the service in the potential clouding computing environment. In our research we choose two data sets, H1N1 VH protein database and Human protein database then compare CUDA-SW and CUDA-SW with filter, we called CUDA-SWf we can obtain up to 41% performance improve from reduce unnecessary sequence alignments.

原文English
主出版物標題CloudCom 2012 - Proceedings
主出版物子標題2012 4th IEEE International Conference on Cloud Computing Technology and Science
頁面735-740
頁數6
DOIs
出版狀態Published - 2012
事件2012 4th IEEE International Conference on Cloud Computing Technology and Science, CloudCom 2012 - Taipei, Taiwan
持續時間: 3 12月 20126 12月 2012

出版系列

名字CloudCom 2012 - Proceedings: 2012 4th IEEE International Conference on Cloud Computing Technology and Science

Conference

Conference2012 4th IEEE International Conference on Cloud Computing Technology and Science, CloudCom 2012
國家/地區Taiwan
城市Taipei
期間3/12/126/12/12

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