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Order and correlations in genomic DNA sequences. The spectral approach

 a,  b
a Pushkov Institute of Terrestrial Magnetism, Ionosphere and Radio Wave Propagation, Russian Academy of Sciences, Kaluzhskoe shosse 4, Troitsk, Москва, 108840, Russian Federation
b State Scientific Center of the Russian Federation ‘Troitsk Institute for Innovation and Fusion Research’, Troitsk, Moscow Region, Russian Federation

The structural analysis of genomic DNA sequences is discussed in the framework of the spectral approach, which is sufficiently universal due to the reciprocal correspondence and mutual complementarity of Fourier transform length scales. The spectral characteristics of random sequences of the same nucleotide composition possess the property of self-averaging for relatively short sequences of length M \geqslant 100-300. Comparison with the characteristics of random sequences determines the statistical significance of the structural features observed. Apart from traditional applications to the search for hidden periodicities, spectral methods are also efficient in studying mutual correlations in DNA sequences. By combining spectra for structure factors and correlation functions, not only integral correlations can be estimated but also their origin identified. Using the structural spectral entropy approach, the regularity of a sequence can be quantitatively assessed. A brief introduction to the problem is also presented and other major methods of DNA sequence analysis described.

Fulltext pdf (712 KB)
Fulltext is also available at DOI: 10.1070/PU2000v043n01ABEH000611
PACS: 02.50.−r, 05.10.−a, 87.10.+e, 87.14.Gg (all)
DOI: 10.1070/PU2000v043n01ABEH000611
URL: https://ufn.ru/en/articles/2000/1/c/
000086055100003
Citation: Lobzin V V, Chechetkin V R "Order and correlations in genomic DNA sequences. The spectral approach" Phys. Usp. 43 55–78 (2000)
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Оригинал: Лобзин В В, Чечеткин В Р «Порядок и корреляции в геномных последовательностях ДНК. Спектральный подход» УФН 170 57–81 (2000); DOI: 10.3367/UFNr.0170.200001c.0057

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  1. Lainscsek X, Taher L 24 (4) (2023)
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  5. Grønbæk Ch, Liang Yu et al 10 e13666 (2022)
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  9. Raju C, Koduru S K, Yasaswini G Recent Developments in Applied Microbiology and Biochemistry (2021) p. 105
  10. Chechetkin V R, Lobzin V V Fluct. Noise Lett. 19 2050019 (2020)
  11. Korotkov E V, Kamionskaya A M, Korotkova M A Lecture Notes In Computer Science Vol. Bioinformatics Research and ApplicationsSearch for Tandem Repeats in the First Chromosome from the Rice Genome12304 Chapter 26 (2020) p. 291
  12. Chechetkin V R, Lobzin V V Journal Of Biomolecular Structure And Dynamics 37 2322 (2019)
  13. Korotkov E V, Korotkova M A Lecture Notes In Computer Science Vol. Bioinformatics and Biomedical EngineeringSearch of Regions with Periodicity Using Random Position Weight Matrices in the Genome of C. elegans10209 Chapter 40 (2017) p. 445
  14. Chechetkin V R, Lobzin V V Journal Of Theoretical Biology 426 162 (2017)
  15. Frenkel F E, Skryabin K G, Korotkov E V J. Phys.: Conf. Ser. 937 012013 (2017)
  16. Pugacheva V, Korotkov A, Korotkov E 15 381 (2016)
  17. Zhang J, Zhang W, Yang H J Biol Phys 42 99 (2016)
  18. Korotkov E V, Korotkova M A BIOPHYSICS 60 876 (2015)
  19. Balakirev E S, Chechetkin V R et al Methods In Molecular Biology Vol. PseudogenesComputational Methods of Identification of Pseudogenes Based on Functionality: Entropy and GC Content1167 Chapter 4 (2014) p. 41
  20. Vinga S Briefings In Bioinformatics 15 376 (2014)
  21. Kravatskaya G I, Chechetkin V R et al Genomics 101 1 (2013)
  22. Chechetkin V R Physics Letters A 377 3312 (2013)
  23. Chalei M B, Chaley M B Math.Biol.Bioinf. 8 502 (2013)
  24. Simakova M N, Simakov N N Mol Biol 47 307 (2013)
  25. Zhang Sh, Xu J, Wei Ch J Biosci 37 19 (2012)
  26. Qi Ya, Jin N, Ai D 10 230 (2012)
  27. Nunes Miriam CS, Wanner E F, Weber G BMC Genomics 12 (S4) (2011)
  28. Titov I I, Vorozheykin P S Russ J Genet Appl Res 1 308 (2011)
  29. Chechetkin V R Physics Letters A 375 1729 (2011)
  30. Kravatskaya G I, Kravatsky Y V et al Genomics 98 223 (2011)
  31. Galleani L, Garello R IEEE Trans. Inform. Theory 56 771 (2010)
  32. Mathematics of Bioinformatics 1 (2010) p. 180
  33. Shelenkov A, Korotkov E Computational Biology And Chemistry 33 196 (2009)
  34. Duan G-Y, Gao Sh et al 2009 3rd International Conference on Bioinformatics and Biomedical Engineering, (2009) p. 1
  35. Paar V, Pavin N et al BMC Bioinformatics 9 (1) (2008)
  36. Illingworth Ch J R, Parkes K E et al Biophysical Chemistry 133 28 (2008)
  37. Larionov S, Loskutov A, Ryadchenko E 18 (1) (2008)
  38. Swati D J. Biosci. 32 1169 (2007)
  39. Chechetkin V R, Lobzin V V Journal Of Biomolecular Structure And Dynamics 24 189 (2006)
  40. Larionov S A, Loskutov A Yu, Ryadchenko E V Dokl. Phys. 50 634 (2005)
  41. Balakirev E S, Chechetkin V R et al 22 2063 (2005)
  42. Laskin A A, Kudryashov N A et al Computational Biology And Chemistry 29 229 (2005)
  43. Simakova M N, Simakov N N Mol Biol 39 284 (2005)
  44. Laskin A A, Kudryashov N A et al Mol Biol 39 372 (2005)
  45. Chechetkin V R, Lobzin V V Physics Letters A 328 79 (2004)
  46. Moreira A Theoretical Computer Science 322 297 (2004)
  47. Luo L, Li H, Zhang L Comp Funct Genom 4 318 (2003)
  48. Korotkov E V, Korotkova M A, Kudryashov N A Physics Letters A 312 198 (2003)
  49. Balakirev E S, Chechetkin V R et al 164 533 (2003)
  50. Chechetkin V R Journal Of Theoretical Biology 222 177 (2003)
  51. Balakirev E S, Ayala F J Annu. Rev. Genet. 37 123 (2003)
  52. ALDANA-GONZÁLEZ M, COCHO G et al Journal Of Theoretical Biology 220 27 (2003)
  53. Holste D, Grosse I, Herzel H Phys. Rev. E 64 (4) (2001)
  54. Kirillova O V Physics Letters A 274 247 (2000)
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