Literature DB >> 23345818

Random fields approach to the study of DNA chains.

Janusz Szczepański1, Tomasz Michałek.   

Abstract

We apply the random field theory tothe study of DNA chains which we assume tobe trajectories of a stochastic process. Weconstruct statistical potential betweennucleotides corresponding to theprobabilities of those trajectories thatcan be obtained from the DNA data basecontaining millions of sequences. It turnsout that this potential has aninterpretation in terms of quantitiesnaturally arrived at during the study ofevolution of species i.e. probabilities ofmutations of codons. Making use of recentlyperformed statistical investigations of DNAwe show that this potential has differentqualitative properties in coding andnoncoding parts of genes. We apply ourmodel to data for various organisms andobtain a good agreement with the resultsjust presented in the literature. We alsoargue that the coding/noncoding boundariescan corresponds to jumps of the potential.

Keywords:  DNA chain; codons; entropy; exons; introns; mutation; random field; stochastic process

Year:  2003        PMID: 23345818      PMCID: PMC3456839          DOI: 10.1023/A:1022508206826

Source DB:  PubMed          Journal:  J Biol Phys        ISSN: 0092-0606            Impact factor:   1.365


  11 in total

Review 1.  Coding sequence evolution.

Authors:  M Kreitman; J M Comeron
Journal:  Curr Opin Genet Dev       Date:  1999-12       Impact factor: 5.578

2.  Base opening in RNA and DNA duplexes: implication for RNA stability.

Authors:  Y Z Chen; V Mohan; R H Griffey
Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  2000-05

3.  Nonlinear modeling technique for the analysis of DNA chains.

Authors:  J Barral P; A Hasmy; J Jiménez; A Marcano
Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  2000-02

4.  Long-range correlations between DNA bending sites: relation to the structure and dynamics of nucleosomes.

Authors:  Benjamin Audit; Cedric Vaillant; Alain Arneodo; Yves d'Aubenton-Carafa; Claude Thermes
Journal:  J Mol Biol       Date:  2002-03-01       Impact factor: 5.469

5.  Chemically driven traveling waves in DNA.

Authors:  T Lipniacki
Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  1999-12

6.  Characterizing long-range correlations in DNA sequences from wavelet analysis.

Authors: 
Journal:  Phys Rev Lett       Date:  1995-04-17       Impact factor: 9.161

7.  Evolution of long-range fractal correlations and 1/f noise in DNA base sequences.

Authors: 
Journal:  Phys Rev Lett       Date:  1992-06-22       Impact factor: 9.161

8.  Long-range correlations in nucleotide sequences.

Authors:  C K Peng; S V Buldyrev; A L Goldberger; S Havlin; F Sciortino; M Simons; H E Stanley
Journal:  Nature       Date:  1992-03-12       Impact factor: 49.962

9.  Long-range correlations in DNA.

Authors:  C A Chatzidimitriou-Dreismann; D Larhammar
Journal:  Nature       Date:  1993-01-21       Impact factor: 49.962

10.  Long-range correlation properties of coding and noncoding DNA sequences: GenBank analysis.

Authors:  S V Buldyrev; A L Goldberger; S Havlin; R N Mantegna; M E Matsa; C K Peng; M Simons; H E Stanley
Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  1995-05
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  1 in total

1.  On the existence of wavelet symmetries in archaea DNA.

Authors:  Carlo Cattani
Journal:  Comput Math Methods Med       Date:  2011-11-28       Impact factor: 2.238

  1 in total

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