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)


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.





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.


  1. 1.
    Rombauts, S., Déhais, P., Van Montagu, M., Rouzé, P.: PlantCARE, a plant cis-acting regulatory element database. Nucleic Acids Res. 27, 295–296 (1999)CrossRefGoogle Scholar
  2. 2.
    Das, M.K., Dai, H.-K.: A survey of DNA motif finding algorithms. BMC Bioinform. 8, 1 (2007)CrossRefGoogle Scholar
  3. 3.
    Perera, P., Ragel, R.: Accelerating motif finding in DNA sequences with multicore CPUs. In: 2013 IEEE 8th International Conference on Industrial and Information Systems, pp. 242–247 (2013)Google Scholar
  4. 4.
    Chauhan, R., Agarwal, P.: A review: applying genetic algorithms for motif discovery. Int. J. Comput. Technol. Appl. 3, 1510–1515 (2012)Google Scholar
  5. 5.
    Seeja, K.: AISMOTIF-an artificial immune system for DNA motif discovery. arXiv preprint arXiv:1107.1128 (2011)
  6. 6.
    Keich, U., Pevzner, P.A.: Finding motifs in the twilight zone. In: Proceedings of the Sixth Annual International Conference on Computational Biology, pp. 195–204 (2002)Google Scholar
  7. 7.
    Buhler, J., Tompa, M.: Finding motifs using random projections. J. Comput. Biol. 9, 225–242 (2002)CrossRefGoogle Scholar
  8. 8.
    Price, A., Ramabhadran, S., Pevzner, P.A.: Finding subtle motifs by branching from sample strings. Bioinformatics 19, ii149–ii155 (2003)CrossRefGoogle Scholar
  9. 9.
    Faheem, H.: Accelerating motif finding problem using grid computing with enhanced brute force. In: The 12th International Conference on Advanced Communication Technology (ICACT), pp. 197–202 (2010)Google Scholar
  10. 10.
    Chen, C., Schmidt, B., Weiguo, L., Müller-Wittig, W.: GPU-MEME: using graphics hardware to accelerate motif finding in DNA sequences. In: IAPR International Conference on Pattern Recognition in Bioinformatics, pp. 448–459 (2008)Google Scholar
  11. 11.
    Farouk, Y., Faheem, H., ElDeeb, T.: Massively Parallelized DNA Motif Search on FPGA. INTECH Open Access Publisher (2011)Google Scholar
  12. 12.
    Steinfadt, S.I.: SWAMP+: enhanced Smith-Waterman search for parallel models. In: 2012 41st International Conference on Parallel Processing Workshops (ICPPW), pp. 62–70 (2012)Google Scholar
  13. 13.
    Seliem, A.G., El-Wafa, W.A., Hamed, H.F.A.: Hardware acceleration of Smith-Waterman algorithm for short read DNA alignment using FPGA. In: Presented at the COMPSAC 2016: The 40th IEEE Computer Society International Conference on Computers, Software & Applications, Atlanta, Georgia, USA (2016)Google Scholar

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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