ISSN:
0392-6737
Keywords:
General, theoretical, and mathematical biophysics (including logic of biosystems, quantum biology, and relevant aspects of thermodynamics, information theory, cybernetics, and bionics)
;
Statistical mechanics
;
Conference proceedings
Source:
Springer Online Journal Archives 1860-2000
Topics:
Physics
Notes:
Summary We present evidence supporting the idea that the DNA sequence in genes containingnoncoding regions is correlated, and that the correlation is remarkably long range-indeed, base pairsthousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene; we utilize this fact to build aCoding Sequence Finder algorithm, which uses statistical ideas to locate the coding regions of an unknown DNA sequence. We resolve the problem of the «non-stationarity» feature of the sequence of base pairs (that the relative concentration of purines and pyrimidines changes in different regions of the mosaic-like chain) by describing a new algorithm calledDetrended Fluctuation Analysis (DFA). We address the claim of Voss that there is no difference in the statistical properties of coding and noncoding regions of DNA by systematically applying the DFA algorithm, as well as standard FFT analysis, to every DNA sequence (33 301 coding and 29 453 non-coding) in the entire GenBank database. We describe a simple model to account for the presence of long-range power law correlations (and the systematic variation of the scaling exponent α with evolution) which is based upon a generalization of the classic Lévy walk. Finally, we describe briefly some recent work showing that thenoncoding sequences have certain statistical features in common with natural languages. Specifically, we adapt to DNA the Zipf approach to analyzing linguistic texts, and the Shannon approach to quantifying the «redundancy» of a linguistic text in terms of a measurable entropy function. We suggest that noncoding regions in eukaryotes may display a smaller entropy and larger redundancy than coding regions for plants and invertebrates, further supporting the possibility that noncoding regions of DNA may carry biological information.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1007/BF02462019
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