Spectral densities and frequencies in the power spectrum of higher order repeat alpha satellite in human DNA molecule

Paar, Vladimir; Pavin, Nenad; Basar, Ivan; Rosandić, Marija; Luketin, Ivica; Durajlija-Žinić, Sonja (2004) Spectral densities and frequencies in the power spectrum of higher order repeat alpha satellite in human DNA molecule. Croatica Chemica Acta, 77 (1-2). pp. 73-81. ISSN 0011-1643

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Abstract

Fast Fourier transform was applied to the central segment of a fully sequenced genomic segment from the centromeric region in human chromosome 7 (GenBank/AC017075.8, 193277 bp), which is characterized by alpha satellite higher order repeats (HOR). Frequencies and spectral densities were computed for all prominent peaks in the Fourier spectrum. We have additionally introduced a peak to noise ratio as effective spectral density in order to account for frequency variations of the noise level. We have shown that a very good description of computed Fourier frequencies can be obtained by using the multiple formula with the fundamental frequency corresponding to the 2734-bp HOR sequence. The peak at f(16) corresponds to the 171-bp monomer. Above the frequency f(16), the most pronounced peaks are mostly at multiples of f(16) (monomer-multiples). The lowest sixteen monomer-multiples kf(16) are locally dominant in spectral densities. The first monomer-multiple that is not locally dominant in spectral density is at k = 17. Above k = 27, the maximum of spectral density is systematically shifted to several neighboring higher frequency multiples. On the basis of the Fourier spectrum, the 171-bp monomer unit was subdivided into three approximately 57-bp subrepeats, which were further subdivided into 12-bp, 14-bp and 17-bp basic subrepeats.

Item Type:	Article
Uncontrolled Keywords:	human DNA; alpha satellite; higher order repeat; Fourier spectrum; long-range correlations; nucleotide-sequences; human chromosome-7; biological sequences; fractal correlations; 1/f-alpha spectrum; genomic sequences; escherichia-coli; fourier-analysis; periodicities
Subjects:	NATURAL SCIENCES > Chemistry
Divisions:	Division of Organic Chemistry and Biochemistry
Projects:	Project title Project leader Project code Project type Nuklearna struktura, kaos i granična područja Vladimir Paar 0119250 MZOS
Depositing User:	Bojan Macan
Date Deposited:	12 Nov 2013 13:44
URI:	http://fulir.irb.hr/id/eprint/929

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