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An Efficient PHSW-DC Algorithm for Solving Motif Finding Problem in TP53 Cancer Gene

  • Asmaa G. Seliem
  • Wael Abouelwafa
  • Hesham F. Hamed
Conference paper
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 753)

Abstract

Bioinformatics scientists are interested in a computational tools that identifies frequency occurring substrings (motifs), which hypothetically have a significant function in whole genome for Deoxyribonucleic Acid (DNA) sequence analysis. This paper proposed a novel algorithm based on Smith Waterman algorithm using the technique of divide and Conquer (HPSW-DC). Both software and hardware accelerators are introduced to accelerate the motif finding algorithms. This paper implements this algorithm on Field Programmable Gate Array (FPGA), which needs hardware specialists to design such systems. A parallel tri-sequence technique decrease the resource utilization, improves the accuracy, increase the computation throughput and accelerate the performance moreover, it enables an alignment for big data available for a complete gene. The proposed algorithm had been synthesize using Xilinx ZynQ7000 which gave us 43 ns execution time, 14% utilization at 869.944 MHz frequency and 72 GCUPS for tetra-nucleotide.

Keywords

DNA Motif PHSW-DC ZYNQ7000 

Notes

Acknowledgment

The authors would like to thank Prof. Kamel H. Rahouma, Department of Electrical and Communication Engineering, minia University, Egypt for his support of this study.

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Electrical Engineering Department, Faculty of EngineeringMinia UniversityMinyaEgypt
  2. 2.Bio-Medical Engineering Department, Faculty of EngineeringMinia UniversityMinyaEgypt

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