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A New Way to Find Similarity/Dissimilarity of DNA Sequences on the Basis of Dinucleotides Representation

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Computational Advancement in Communication Circuits and Systems

Part of the book series: Lecture Notes in Electrical Engineering ((LNEE,volume 335))

Abstract

In this paper, we have introduced a new way of representation of dinucleotides. They are directly represented by two-dimensional coordinates (x, y) in the Euclidean plane. By writing \(z=x\times y\), ultimately the representation is given by three-dimensional coordinates (x, y, z). Based on the variances of cumulative values \( x ' ,y ' ,z ' \) of x, y, and z respectively, a measure is determined to compare coding sequences of β-globin genes of 11 species. We have also used another measure for similar comparison of sequences. This is based on the probability distribution of dinucleotides occurring in the sequence. Finally, we have compared the similarity/dissimilarity matrix obtained under above two measures by the method of correlation coefficient.

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References

  1. E. Hamori, J. Ruskin, H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences. J. Biol. Chem. 258, 1318–1327 (1983)

    Google Scholar 

  2. A. Nandy, M. Harle, S.C. Basak, Mathematical descriptors of DNA sequences: development and applications. ARKIVOC 9, 211–238 (2006)

    Article  Google Scholar 

  3. C.T. Zhang, R. Zhang, Analysis of distribution of bases in the coding sequences by a diagrammatic technique. Nucl. Acids Res. 19, 6313–6317 (1991)

    Article  Google Scholar 

  4. R. Zhang, C.T. Zhang, Z curves, an intuitive tool for visualizing and analyzing the DNA sequences. J. Biomol. Struct. Dyn. 11, 767–782 (1994)

    Article  Google Scholar 

  5. A. Nandy, A new graphical representation and analysis of DNA sequence structure: I. methodology and application to globin genes. Curr. Sci. 66, 309–314 (1994)

    Google Scholar 

  6. Z.J. Zhang, DV–Curve: a novel intuitive tool for visualizing and analyzing DNA sequences. Bioinformatics 25, 1112–1117 (2009)

    Article  Google Scholar 

  7. F.B. Guo, H.Y. Ou, C.T. Zhang, ZCURVE: a new system for recognizing protein–coding genes in bacterial and archaeal genomes. Nucl. Acids. Res. 31, 1780–1789 (2003)

    Article  Google Scholar 

  8. J.F. Yu, X. Sun, J.H. Wang, TN curve: a novel 3D graphical representation of DNA sequence based on trinucleotides and its applications, J. Theoret. Biol. (In press) doi:10.1016/j.jtbi.2009.08.005

  9. X.Q. Liu, Q. Dai, Z.L. Xiu, T.M. Wang, PNN–curve: a new 2D graphical representation of DNA sequences and its application. J. Theoret. Biol. 243, 555–561 (2006)

    Article  MathSciNet  Google Scholar 

  10. X.Q. Qi, J. Wen, Z.H. Qi, New 3D graphical representation of DNA sequence based on dual nucleotides. J. Theoret. Biol. 249, 681–690 (2007)

    Article  MathSciNet  Google Scholar 

  11. Z.H. Qi, T.R. Fan, PN–curve: a 3D graphical representation of DNA sequences and their numerical characterization. Chem. Phys. Lett. 442, 434–440 (2007)

    Article  Google Scholar 

  12. Z. Cao, B. Liao, R.F. Li, A Group of 3D graphical representation of DNA sequences based on dual nucleotides. Int. J. Quantum Chem. 108, 1485–1490 (2008)

    Article  Google Scholar 

  13. Z.B. Liu, B. Liao, W. Zhu, G.H. Huang, A 2–D graphical representation of DNA sequence based on dual nucleotides and its application. Int. J. Quantum Chem. 109, 948–958 (2009)

    Article  Google Scholar 

  14. J.F. Yu, J.H. Wang, X. Sun, Analysis of similarities/dissimilarities of DNA sequences based on a novel graphical representation. State Key Laboratory of Bioelectronics

    Google Scholar 

  15. B. Liao, T.M. Wang, 3–D graphical representation of DNA sequences and their numerical characterization. J. Mol. Struct. (Theochem) 681, 209–212 (2004)

    Article  Google Scholar 

  16. R. Chi, K.Q. Ding, Novel 4D numerical representation of DNA sequences. Chem. Phys. Lett. 407, 63–67 (2005)

    Article  Google Scholar 

  17. Y.H. Yao, X.Y. Nan, T.M. Wang, A new 2D graphical representation—Classification curve and the analysis of similarity/dissimilarity of DNA sequences. J. Mol. Struct. (Theochem) 764, 101–108 (2006)

    Article  Google Scholar 

  18. B. Liao, K.Q. Ding, A 3D graphical representation of DNA sequences and its application. Theoret. Comput. Sci. 358, 56–64 (2006)

    Article  MATH  MathSciNet  Google Scholar 

  19. B. Liao, T.M. Wang, Analysis of similarity/dissimilarity of DNA sequences based on non-overlapping triplets of nucleotide bases. J. Chem. Inf. Comput. Sci. 44, 1666–1670 (2004)

    Article  MathSciNet  Google Scholar 

  20. W.Y. Chen, B. Liao, Y.H. Liu, W. Zhu, Z.Z. Su, A numerical representation of DNA sequence and its applications. MATCH Commun. Math. Comput. Chem. 60, 291–300 (2008)

    MATH  MathSciNet  Google Scholar 

  21. B. Liao, W. Zhu, Y. Liu, 3D graphical representation of DNA sequence without degeneracy and its applications in constructing phylogenic tree. MATCH Commun. Math. Comput. Chem. 56, 209–216 (2006)

    MATH  MathSciNet  Google Scholar 

  22. B. Liao, C. Zeng, F.Q. Li, Y. Tang, Analysis of similarity/dissimilarity of DNA sequences based on dual nucleotides. MATCH Commun. Math. Comput. Chem. 59, 647–652 (2008)

    MATH  MathSciNet  Google Scholar 

  23. M. Randic, J. Zupan, D. Vikic-Topic, D. Plavsic, A novel unexpected use of a graphical representation of DNA: graphical alignment of DNA sequences. Chem. Phys. Lett. 431, 375–379 (2006)

    Article  Google Scholar 

  24. Y. Guo, T.M. Wang, A new method to analyze the similarity of the DNA sequences. J. Mol. Struct. (Theochem) 853, 62–67 (2008)

    Article  Google Scholar 

  25. P.A. He, J. Wang, Characteristic sequences for DNA primary sequence. J. Chem. Inf. Comput. Sci. 42, 1080–1085 (2002)

    Article  Google Scholar 

  26. J. Wang, Y. Zhang, Characterization and similarity analysis of DNA sequences based on mutually direct–complementary triplets. Chem. Phys. Lett. 425, 324–328 (2006)

    Article  Google Scholar 

  27. Y.S. Zhang, W. Chen, Invariants of DNA sequences based on 2DD–curves. J. Theoret. Biol. 242, 382–388 (2006)

    Article  MathSciNet  Google Scholar 

  28. J.F. Yu, X. Sun, J.H. Wang, TN curve: a novel 3D graphical representation of DNA sequence based on trinucleotides and its applications. Med. Eng. Phy. 459–460 (2009)

    Google Scholar 

  29. M. Randic, M. Vracko, N. Lers, D. Plavsic, Novel 2–D graphical representation of DNA sequences and their numerical characterization. Chem. Phys. Lett. 368, 1–6 (2003)

    Article  Google Scholar 

  30. B. Liao, T.M. Wang, Analysis of similarity/dissimilarity of DNA sequences based on 3–D graphical representation. Chem. Phys. Lett. 388, 195–200 (2004)

    Article  Google Scholar 

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Authors and Affiliations

  1. Department of Computer Science and Engineering, Narula Institute of Technology, Kolkata, India

    Subhram Das, Subhra Palit, Anindya Raj Mahalanabish & Nobhonil Roy Choudhury

Authors
  1. Subhram Das
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  2. Subhra Palit
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  3. Anindya Raj Mahalanabish
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  4. Nobhonil Roy Choudhury
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Corresponding author

Correspondence to Subhram Das .

Editor information

Editors and Affiliations

  1. School of Electronics & Computer Science, University of Southampton, Southampton, United Kingdom

    Koushik Maharatna

  2. Design & Growth, Institute of Materials Research & Engg, Singapore, Singapore

    Goutam Kumar Dalapati

  3. Electronics and Telecommunication Engg, Jadavpur University, Kolkata, West Bengal, India

    P K Banerjee

  4. Electronics and Electrical Communication, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India

    Amiya Kumar Mallick

  5. Centre for Millimeter Wave Semiconductor Devices and Systems, Defence Research and Development Org., Kolkata, West Bengal, India

    Moumita Mukherjee

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Das, S., Palit, S., Mahalanabish, A.R., Choudhury, N.R. (2015). A New Way to Find Similarity/Dissimilarity of DNA Sequences on the Basis of Dinucleotides Representation. In: Maharatna, K., Dalapati, G., Banerjee, P., Mallick, A., Mukherjee, M. (eds) Computational Advancement in Communication Circuits and Systems. Lecture Notes in Electrical Engineering, vol 335. Springer, New Delhi. https://doi.org/10.1007/978-81-322-2274-3_19

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  • DOI: https://doi.org/10.1007/978-81-322-2274-3_19

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  • Publisher Name: Springer, New Delhi

  • Print ISBN: 978-81-322-2273-6

  • Online ISBN: 978-81-322-2274-3

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