Skip to main content
SpringerLink
Log in

Developing a mathematical method to search for latent periodicity in protein amino-acid sequences with deletions and insertions

  • Molecular Biophysics
  • Published:
Biophysics Aims and scope Submit manuscript

Abstract

A mathematical method has been developed in order to search for latent periodicity in protein amino-acid and other symbolical sequences using dynamic programming and random matrices. The method allows the detection of the latent periodicity with insertions and deletions at positions that are unknown beforehand. The developed method has been applied to search for the periodicity in the amino-acid sequences of several proteins and in the euro/dollar exchange rate since 2001. The presence of a long period with insertions and deletions in amino-acid sequences is shown. The period length of seven amino acids is observed in the proteins that contain supercoiled regions (a coiled-coil structure) as well as of six, five, or more amino acids. The existence of the period length of 6 and 7 days, as well as 24 and 25 h in the analyzed financial time series is observed; note that this periodicity is detectable only for insertions and deletions. The causes that underlie the occurrence of the latent periodicity with insertions and deletions in amino-acid sequences and financial time series are discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. R. Ekblom and J. B. W. Wolf, Evol. Appl. 7 (9), 1026 (2014).

    Article  Google Scholar 

  2. E. V. Korotkov, M. A. Korotkova, and N. A. Kudryashov, Phys. Lett. A: Gen. At. Solid State Phys. 312 (3–4), 198 (2003).

    Article  MathSciNet  MATH  Google Scholar 

  3. E. V. Korotkov, M. A. Korotkova, and N. A. Kudryashov, Mol. Biol. (Moscow) 37 (3), 436 (2003).

    Article  MathSciNet  Google Scholar 

  4. V. Afreixo, P. J. S. G. Ferreira, and D. Santos, Digit. Signal Process 14 (6), 523 (2004).

    Article  Google Scholar 

  5. G. I. Kravatskaya, Y. V. Kravatsky, V. R. Chechetkin, and V. G. Tumanyan, Genomics 98 (3), 223 (2011).

    Article  Google Scholar 

  6. V. V. Lobzin, Usp. Fiz. Nauk 170 (1), 57 (2000).

    Article  Google Scholar 

  7. T. Meng, A. T. Soliman, M.-L. Shyu, et al., IEEE/ACM Trans. Comput. Biol. Bioinform. 10 (6), 1442 (2013).

    Article  Google Scholar 

  8. M. de Sousa Vieira, Phys. Rev. E: Stat. Phys. Plasmas. Fluids. Relat. Interdiscip. Topics 60 (5, Pt. B), 5932 (1999).

    Article  Google Scholar 

  9. Y. M. Suvorova, M. A. Korotkova, and E. V. Korotkov, Comput. Biol. Chem. 53 (Pt. A), 43 (2014).

    Article  Google Scholar 

  10. S. Tiwari, S. Ramachandran, A. Bhattacharya, et al., Comput. Appl. Biosci. CABIOS 13 (3), 263 (1997).

    Google Scholar 

  11. A. Agrawal and X. Huang, IEEE/ACM Trans. Comput. Biol. Bioinform. 8 (1), 194 (2009).

    Article  Google Scholar 

  12. T. F. Smith and M. S. Waterman, J. Mol. Biol. 147, 195 (1954).

    Article  Google Scholar 

  13. A. Shelenkov, K. Skryabin, and E. Korotkov, DNA Res. 13 (3), 89 (2006).

    Article  Google Scholar 

  14. Information Theory and Statistics, Ed. by S. Kullback (Dover Publ., New York, 1997).

  15. V. O. Polyanovsky, M. A. Roytberg, and V. G. Tumanyan, Algorithms Mol. Biol. 6 (1), 25 (2011).

    Article  Google Scholar 

  16. B. Boeckmann, A. Bairoch, R. Apweiler, et al., Nucleic Acids Res. 31 (1), 365 (2003).

    Article  Google Scholar 

  17. A. V. Kajava, J. Struct. Biol. 179 (3), 279 (2012).

    Article  Google Scholar 

  18. B. Hochhut, C. Wilde, G. Balling, et al., Mol. Microbiol. 61 (3), 584 (2006).

    Article  Google Scholar 

  19. K. Tamura, Y. Fukao, M. Iwamoto, et al., Plant Cell 22 (12), 4084 (2010).

    Article  Google Scholar 

  20. J. M. Mason and K. M. Arndt, Chembiochem 5 (2), 170 (2004).

    Article  Google Scholar 

  21. A. Copeland, S. Lucas, A. Lapidus, et al., Submitted to EMBL/GenBank/DDBJ databases. US DOE Jt. Genome Inst. (2005)

    Google Scholar 

  22. P. Enkhbayar, K. Hikichi, M. Osaki, et al., Proteins 64 (3), 691 (2006).

    Article  Google Scholar 

  23. P. Fabian, V. S. Chauhan, and S. Pongor, Biochim. Biophys. Acta 1208 (1), 89 (1994)

    Article  Google Scholar 

  24. T. J. Brickman, C. E. Barry, and T. Hackstadt, J. Bacteriol. 175 (14), 4274 (1993).

    Google Scholar 

  25. K. K. Jernigan and S. R. Bordenstein, Peer J 3, e732c (2015).

    Article  Google Scholar 

  26. J. Jorda, B. Xue, V. N. Uversky, and A. V. Kajava, FEBS J. 277 (12), 2673 (2010).

    Article  Google Scholar 

  27. M. N. Fodje and S. Al-Karadaghi, Protein Eng. Des. Sel. 15 (5), 353 (2002).

    Article  Google Scholar 

  28. M. S. Lee, G. P. Gippert, K. V. Soman, et al., Science 245 (4918), 635 (1989).

    Article  ADS  Google Scholar 

  29. M. R. Sawaya, W. M. Wojtowicz, I. Andre, et al., Cell 134 (6), 1007 (2008).

    Article  Google Scholar 

  30. P. A. Elkins, Y. Sen Ho, W. W. Smith, et al., Acta Crystallogr. D: Biol. Crystallogr. 58 (Pt 7), 1182 (2002).

    Article  Google Scholar 

  31. A. De Grassi and F. D. Ciccarelli, Genome Biol. 10 (12), R137c (2009).

    Google Scholar 

  32. A. K. Bjorklund, D. Ekman, and A. Elofsson, PLoS Comput. Biol. 2 (8), e114c (2006).

    Article  ADS  Google Scholar 

  33. F. Halberg, Annu. Rev. Physiol. 31 (1), 675 (1969).

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Fundamental Bases of Biotechnology Federal Center, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7/1, Moscow, 117312, Russia

    E. V. Korotkov

  2. National Research Nuclear University, Moscow Engineering Physics Institute, Kashirskoe sh. 31, Moscow, 105409, Russia

    E. V. Korotkov & M. A. Korotkova

Authors
  1. E. V. Korotkov
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. M. A. Korotkova
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to E. V. Korotkov.

Additional information

Original Russian Text © E.V. Korotkov, M.A. Korotkova, 2015, published in Biofizika, 2015, Vol. 60, No. 6, pp. 1057–1068.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Korotkov, E.V., Korotkova, M.A. Developing a mathematical method to search for latent periodicity in protein amino-acid sequences with deletions and insertions. BIOPHYSICS 60, 876–885 (2015). https://doi.org/10.1134/S0006350915060159

Download citation

  • Received:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S0006350915060159

Keywords

Search

Navigation