The study of DNA sequences by their sequences of twist angles

ABSTRACT:To obtain new insight into the nature of the correlations in distributions of nucleotides in DNA sequences, an efficient algorithm is presented by means of which one can generate nucleotide sequences with prescribed correlational properties. It is demonstrated in the case of human T-cell receptor beta chain gene segment that by extracting a finite number of parameters from the natural sequence one can generate artificial sequences which reproduce the correct correlational properties. It is shown how the apparent long-range correlations, or-what is equivalent-the 1rf form of the spectral density result due to the arrangement of DNA segments with different functional roles which also differ in composition in terms of nucleotide classes. This approach enables one to get under control the impact of statistical fluctuations which represent a major obstacle in the analyses of finite natural sequences.

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Computer simulation of DNA sequential correlations

Borštnik

Pumpernik

Lukman

1997

Int. J. Quant. Chem.

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The character of the correlations in DNA sequences

Borštnik

1994

Int J of Quantum Chemistry

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Although several authors proposed the existence of long-range correlations in DNA sequences w. Li and K. Kaneko, Europhys. Lett. 17, 655 (1992); R.F. Voss, Phys. Rev. Lett. 68, 3805 (1992); C.-K. Peng et al., Nature 356, 168 (1992)], we claim that the real character of the correlations remains uncertain. To corroborate long-range correlations, one should prove that the correlation functions decay as an inverse power of the distance between the nucleotides in the DNA sequence. Instead of a direct calculation of the correlation functions, one can calculate either the Fourier transforms of the sequences or the characteristics of "DNA walk." In our previous work we pointed out that the character of the results depends upon the way the DNA sequences are chosen. When looking for the correlations separately in introns and separately in exons, we found that the resulting correlations are short range. In this work, we discuss the numerical aspects of two computational approaches: the calculation of correlation function and the evaluation of "DNA walk" characteristics. We present the analytic results for the case of exponential correlations.

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Diagrammatic representation of the distribution of DNA bases and its applications

Zhang

Ren

1991

International Journal of Biological Macromolecules

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The study of DNA sequences by their sequences of twist angles

Cited by 4 publications

References 7 publications

Computer simulation of DNA sequential correlations

Computer simulation of DNA sequential correlations

The character of the correlations in DNA sequences

Diagrammatic representation of the distribution of DNA bases and its applications

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