Reviews of topical problems

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, , 108840, Russian Federation
b State Scientific Center ofthe 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.

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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
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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:   ,    «     . » 170 57–81 (2000); DOI: 10.3367/UFNr.0170.200001c.0057

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