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  • EuPhyJ,98,Arneodo
    Centre de Mathématiques Appliquées École Polytechnique 91128 Palaiseau France European Physical Journal B1 259 263 1998 Abstract We use the wavelet transform to investigate the fractal scaling properties of coding and noncoding human DNA sequences We find that the strength of the long range correlations observed in the introns increases with the guanine cytosine GC content while coding sequences show no such correlations at any GC content However we demonstrate

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-epj98-a.html (2012-11-26)
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  • EuPhyJ,98,Cebrat
    271 276 1998 Abstract We have performed several kinds of DNA walks which often are the first steps for further analysis of DNA structure and long range correlations The DNA walks analysing frequency of G C versus A T cannot indicate the coding strand while purine versus pyrimidine DNA walks or two dimensional A T G C DNA walks in some instances can indicate the coding strand but cannot resolve

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-epj98-c.html (2012-11-26)
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  • JTheoBio,98,Chechetkin
    for the study of correlations in segmented DNA sequences is developed Within this approach the effects of compositional patchiness are separated from the beginning allowing us to display the refined effects of structural coupling between different segments The mutual analysis of Fourier structure spectra and pair correlation functions identifies both the main ranges long short or intermediate and the sources coincident periodicities large scale density variations short memory coupling or

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-jtb98-cl.html (2012-11-26)
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  • Bioinfo,98,Coward
    genome sequencing projects makes it relevant to develop sensitive automatic methods for the identification of repeats Results A new method for finding periodic patterns in biological sequences is presented The method is based on evolutionary distance and phase shifts corresponding to insertions and deletions A given sequence is aligned to itself in a certain sense trying to minimize a distance to periodicity Relationships between different such periodicity measures are discussed

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-bioinfo98-cd.html (2012-11-26)
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  • Cyto&CellGenet,98,Epplen
    have not yielded definitive results Therefore these elements are commonly regarded as genomic junk although they represent assets for innovative methodological approaches and especially for speculations While extensively using microsatellites for genome mapping and genetic relationship analyses it was also realized that certain simple repeats can cause human trinucleotide block expansion diseases Hence these simple repeat elements comprise an exceptional range of biological meaning i e from genetically absolutely neutral

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-ccg98-e.html (2012-11-26)
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  • NAR,98,Grigoriev
    at two points separated by about a half of its length These points coincide with sites of replication origin and terminus for all bacteria where such sites are known The leading strand is found to contain more guanine than cytosine residues This fact is used to predict origin and terminus locations in other bacterial and archaeal genomes Local changes visible as diagram distortions may represent recent genome rearrangements as demonstrated

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-nar98-g.html (2012-11-26)
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  • JBioStruDyn,98,Herzel
    and Sussman Proc Natl Acad Sci USA 77 pp 3816 20 Recently also the negative supercoiling of eubacterial DNA was related to 11 base pair bp periodicity Herzel et al Physica A 249 pp 449 59 Archaeal plasmids and a virus like particle from Sulfolobus are positively supercoiled but the superhelical conformation of archaeal genomic DNA is still uncertain The problem of superhelicity can now be addressed via a comparative

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-jbsd98-h.html (2012-11-26)
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  • JPhyA,98,Holste
    numerical estimates In this paper we focus upon the problem of estimating generalized entropies from finite samples and derive the Bayes estimator of the order q Tsallis entropy including the order 1 i e the Shannon entropy under the assumption of a uniform prior probability density The Bayes estimator yields in general the smallest mean quadratic deviation from the true parameter as compared with any other estimator Exploiting the functional

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-jpa98-h.html (2012-11-26)
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