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  • GeRes,98,Li
    former we show by the size distribution of domains coding density size distribution of open reading frames spatial power spectra and deviation from binomial distribution for C G in large moving windows that there is a strong deviation of the yeast sequences from random sequences For the latter not only do we graphically illustrate the similarity for the above mentioned statistics but we also carry out a rigorous analysis of

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-gr98-l.html (2012-11-26)
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  • PhyRevE,98, Lu
    Abstract In this paper some parametric methods are introduced to characterize the self similarity of DNA sequences Compared with Fourier analysis these methods perform statistically more stably and yield more reliable results Using these methods eight whole genomes of bacteria provided by NCBI are analyzed Long range correlation properties in the nucleotide density distribution along these DNA sequences are explored Estimation results show that the long range correlation structure prevails

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-pre98-l.html (2012-11-26)
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  • JMolEvol,98,McLean
    leading strand in DNA replication is G T rich at codon position 3 in six eubacteria but C T rich in two Mycoplasma species In M genitalium the AT and GC skews are symmetrical around the origin and terminus of replication whereas its GC content variation has been shown to have a centre of symmetry elsewhere in the genome Borrelia burgdorferi and Treponema pallidum show extraordinary extents of base composition

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-jme98-m.html (2012-11-26)
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  • PNAS,98,Mrazek
    asymmetry is not observed in the cyanobacterium Synechocystis sp genome nor in the archaeal genomes of Methanococcus jannaschii Methanobacterium thermoautotrophicum and Archaeoglobus fulgidus A strong strand compositional asymmetry is observed in alpha type but not beta or gamma type human herpesviruses featuring G C downstream of oriL and C G upstream of oriL Dinucleotide relative abundances i e dinucleotide representations normalized by the component nucleotide frequencies are consonant with respect

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-pnas98-mk.html (2012-11-26)
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  • PhyRevLett,98, Roman
    segmentation of DNA sequences into compositionally homogeneous domains is proposed Sequence compositional complexity SCC deals directly with the complex heterogeneity in non stationary DNA sequences The plot of SCC as a function of significance level provides a profile of sequence structure at different length scales SCC is found to be higher in sequences with long range correlation than those without and higher in non coding sequences than coding sequences Furthermore

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-prl98-rbo.html (2012-11-26)
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  • PNAS,98,Wolfe
    of the original genes were retained in duplicate after genome duplication and 70 100 reciprocal translocations occurred between chromosomes produced arrangements of duplicated chromosomal regions very similar to the map of real duplications in yeast An analytical method produced an independent estimate of 84 map disruptions These results imply that many smaller duplicated chromosomal regions exist in the yeast genome in addition to the 55 originally reported We also examined

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-pnas98-sw.html (2012-11-26)
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  • CurrOpGenet,98,Skrabanek
    694 700 1998 Abstract Several eukaryotes including maize yeast and Xenopus are degenerate polyploids formed by relatively recent whole genome duplications Ohno s conjecture that more ancient genome duplications occurred in an ancestor of vertebrates is probably at least partly true but the present shortage of gene sequence and map information from vertebrates makes it difficult to either prove or disprove this hypothesis Candidate paralogous segments in mammalian genomes have

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-cogd98-sw.html (2012-11-26)
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  • JTheoBio,98,Weiss
    codes are tested as such mappings We found hydrophobicity autocorrelation functions to be strongly oscillating Another strong signal is the monotonously decaying alpha helix propensity autocorrelation function Furthermore we detected signals corresponding to an alteration of positively and negatively charged residues at a distance of 3 4 amino acids To look beyond the property codes gained by the methods of physical chemistry mappings yielding a strong correlation signal are sought

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-jtb98-wh.html (2012-11-26)
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