Binary Error Correcting Code for DNA Databank

  • Jagannath Samanta
  • Jaydeb Bhaumik
  • Soma Barman
  • Raj Kumar Maity
Conference paper
Part of the Lecture Notes in Electrical Engineering book series (LNEE, volume 470)

Abstract

Deoxyribonucleic acid (DNA) is the storage media of heredity information of all living species. These DNA molecules store the digital information that comprises the genetic blueprint of living organisms. The DNA databank can be employed in the analysis of genetic diseases, fingerprinting for criminology or genetic genealogy. There is the possibility of soft errors in these DNA databases during the long-term storage purpose. In this chapter, a binary error correcting code (ECC) is used to improve the reliability of stored DNA bases. An encoding and decoding algorithm is proposed for any arbitrary length of DNA sequences. A single error correcting code (280, 256) codec has been designed and implemented. Proposed designs are simulated and synthesized using both FPGA and ASIC platforms.

Keywords

Error correcting code Single error correcting code Deoxyribonucleic acid FPGA and ASIC 

References

  1. 1.
    E.E. May, Comparative analysis of information based models for initiating protein translation in Escherichia coli K-12, M.S. thesis, NCSU, Dec 1998Google Scholar
  2. 2.
    E. May, M. Vouk, D. Nitzer, D. Rosnick, An error-correcting code framework for genetic sequence analysis. J. Franklin Inst. 34, 89–109 (2004)Google Scholar
  3. 3.
    L. Liebovitch, Y. Tao, A. Todorov, L. Levine, Is there an error correcting code in the base sequence in DNA? Biophysical J. 71(3), 1539–1544 (1996)Google Scholar
  4. 4.
    M. Blawat, K. Gaedke, I. Huetter, X.M. Chen, B. Turczyk, S. Inverso, B.W. Pruitt, G.M. Church, Forward error correction for DNA data storage. Procedia Comput. Sci. 80, 1011–1022 (2016)Google Scholar
  5. 5.
    L.C.B. Faria, A.S.L. Rocha, J.H. Kleinschmidt, R. Palazzo, M.C. Silva-Filho, DNA sequences generated by BCH codes over GF(4). Electron. lett. 46(3), 203–204 (2010)Google Scholar
  6. 6.
    L.L. Gatlin, Information Theory and the Living System (Columbia University Press, New York, NY, 1972)Google Scholar
  7. 7.
    I.B. Djordjevic, Classical and quantum error-correction coding in genetics, Quantum Biological Information Theory, pp. 237–269 (2016)Google Scholar
  8. 8.
    P. Reviriego, S. Pontarelli, J.A. Maestro, M. Ottavi, A method to construct low delay single error correction codes for protecting data bits only. IEEE Trans. Comput. Aided Des. Integ. Circ. Syst. 32(3), 479–483 (2013)Google Scholar
  9. 9.
    J.L. Doleac, The effects of DNA databases on crime. Am. Econ. J. Appl. Econ. Life Sci. Soc. Policy 9(1), 165–201 (2017)Google Scholar
  10. 10.
    Advancing justice through DNA technology using DNA solve crimes, U.S. Department of Justice Archives. https://www.justice.gov/archives/ag
  11. 11.
  12. 12.
    I. Murnaghan, The importance of DNA, explore DNA (2017). http://www.exploredna.co.uk/the-importance-dna.html
  13. 13.
    F. Santos, H. Machado, S. Silva, Forensic DNA databases in European countries: is size linked to performance? Life Sci. Soc. Policy 9(1), 4513018 (2013)Google Scholar
  14. 14.
    J.M. Butler, Advanced Topics in Forensic DNA Typing: Methodology (Academic Press, 2011)Google Scholar
  15. 15.
    H. Wallace, The UK national DNA database: balancing crime detection, human rights and privacy, EMBO Report, pp. S26–S30 (2006)Google Scholar
  16. 16.
  17. 17.
    J.L. Doleac, The effects of DNA databases on crime. Am. Econ. J. Appl. Econ. 9(1), 165–201. https://doi.org/10.1257/app.20150043. ISSN 1945-7782
  18. 18.
    A. Oconnor, The claim: identical twins have identical DNA, The New York Times (2008). http://www.nytimes.com/2008/03/11/health/11real.html

Copyright information

© Springer Nature Singapore Pte Ltd. 2017

Authors and Affiliations

  • Jagannath Samanta
    • 1
  • Jaydeb Bhaumik
    • 1
  • Soma Barman
    • 2
  • Raj Kumar Maity
    • 1
  1. 1.Haldia Institute of TechnologyHaldiaIndia
  2. 2.Institute of Radio Physics and ElectronicsUniversity of CalcuttaKolkataIndia

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