Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System
The Smith-Waterman (SW) algorithm has been widely utilized for searching biological sequence databases in bioinformatics. Recently, several works have adopted the graphic card with Graphic Processing Units (GPUs) and their associated CUDA model to enhance the performance of SW computations. However,...
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| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2015-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2015/761063 |
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| _version_ | 1832564225275330560 |
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| author | Yu Liu Yang Hong Chun-Yuan Lin Che-Lun Hung |
| author_facet | Yu Liu Yang Hong Chun-Yuan Lin Che-Lun Hung |
| author_sort | Yu Liu |
| collection | DOAJ |
| description | The Smith-Waterman (SW) algorithm has been widely utilized for searching biological sequence databases in bioinformatics. Recently, several works have adopted the graphic card with Graphic Processing Units (GPUs) and their associated CUDA model to enhance the performance of SW computations. However, these works mainly focused on the protein database search by using the intertask parallelization technique, and only using the GPU capability to do the SW computations one by one. Hence, in this paper, we will propose an efficient SW alignment method, called CUDA-SWfr, for the protein database search by using the intratask parallelization technique based on a CPU-GPU collaborative system. Before doing the SW computations on GPU, a procedure is applied on CPU by using the frequency distance filtration scheme (FDFS) to eliminate the unnecessary alignments. The experimental results indicate that CUDA-SWfr runs 9.6 times and 96 times faster than the CPU-based SW method without and with FDFS, respectively. |
| format | Article |
| id | doaj-art-d5871af52a34446d82b7fb2875237bbc |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2015-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-d5871af52a34446d82b7fb2875237bbc2025-02-03T01:11:32ZengWileyInternational Journal of Genomics2314-436X2314-43782015-01-01201510.1155/2015/761063761063Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative SystemYu Liu0Yang Hong1Chun-Yuan Lin2Che-Lun Hung3School of Electronic Information Engineering, Tianjin University, Tianjin 300072, ChinaSchool of Electronic Information Engineering, Tianjin University, Tianjin 300072, ChinaDepartment of Computer Science and Information Engineering, Chang Gung University, Taoyuan 33302, TaiwanDepartment of Computer Science and Communication Engineering, Providence University, Taichung 43301, TaiwanThe Smith-Waterman (SW) algorithm has been widely utilized for searching biological sequence databases in bioinformatics. Recently, several works have adopted the graphic card with Graphic Processing Units (GPUs) and their associated CUDA model to enhance the performance of SW computations. However, these works mainly focused on the protein database search by using the intertask parallelization technique, and only using the GPU capability to do the SW computations one by one. Hence, in this paper, we will propose an efficient SW alignment method, called CUDA-SWfr, for the protein database search by using the intratask parallelization technique based on a CPU-GPU collaborative system. Before doing the SW computations on GPU, a procedure is applied on CPU by using the frequency distance filtration scheme (FDFS) to eliminate the unnecessary alignments. The experimental results indicate that CUDA-SWfr runs 9.6 times and 96 times faster than the CPU-based SW method without and with FDFS, respectively.http://dx.doi.org/10.1155/2015/761063 |
| spellingShingle | Yu Liu Yang Hong Chun-Yuan Lin Che-Lun Hung Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System International Journal of Genomics |
| title | Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System |
| title_full | Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System |
| title_fullStr | Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System |
| title_full_unstemmed | Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System |
| title_short | Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System |
| title_sort | accelerating smith waterman alignment for protein database search using frequency distance filtration scheme based on cpu gpu collaborative system |
| url | http://dx.doi.org/10.1155/2015/761063 |
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