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

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

2 Scopus citations

Abstract

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.

Original languageEnglish
Title of host publicationCloudCom 2012 - Proceedings
Subtitle of host publication2012 4th IEEE International Conference on Cloud Computing Technology and Science
Pages735-740
Number of pages6
DOIs
StatePublished - 2012
Event2012 4th IEEE International Conference on Cloud Computing Technology and Science, CloudCom 2012 - Taipei, Taiwan
Duration: 3 Dec 20126 Dec 2012

Publication series

NameCloudCom 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
Country/TerritoryTaiwan
CityTaipei
Period3/12/126/12/12

Keywords

  • CUDA
  • GPGPU
  • Smith-Waterman
  • alignment
  • filter
  • sequence

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