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  • Fractal,2000,Provata
    coding parts of DNA sequences are regarded as clusters of connected sites of a random Cantor like set while the non coding parts are regarded as the empty regions of the same set Under this representation we find that higher eucaryotes are mapped on random Cantor sets with fractal dimension around 0 85 while lower organisms are mapped on Cantor sets with fractal dimension 1 This result indicates that the

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-fractal00-p.html (2012-11-26)
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  • StatSci,00,Stoffer
    2000 Abstract The concept of the spectral envelope was recently introduced as a statistical basis for the frequency domain analysis and scaling of qualitative value time series In the process of developing the spectral envelope methodology many other interesting extensions became evident In this article we explain the basic concept and give numerous examples of the usefulness of the technology These examples include analyses of DNA sequences finding optimal transformations

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-ss00-s.html (2012-11-26)
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  • JMolEvol,2000,Tillier
    presentations and quantitative statistical analyses analysis of variance we have found that a significant proportion of the GC and AT skews can be attributed to replication orientation i e the sequence of a gene is influenced by whether it is encoded on the leading or lagging strand This effect of replication orientation on skews is independent of and can be opposite in sign to the effects of transcriptional or translational

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-jme00-t.html (2012-11-26)
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  • JTheoBio,99,Almirantis
    Feb 7 1999 Abstract A method quantifying the randomness of nucleotide sequences is developed based on the introduction of a standard deviation type of quantity involving locally computed means and a length scale around which is assessed the clustering of nucleotides It is pointed out that the value taken by this modified standard deviation may distinguish between coding rich and non coding rich sequences Moreover the approach described herein allows

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-jtb99-a.html (2012-11-26)
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  • JTheoBio,99,Bell
    shorter regions than the corresponding natural sequence For an E coli segment S base accounting is on average contained within a region of 10 kb whereas W base accounting requires regions in excess of 100 kb Accounting requires the entire genome 190 kb in the case of Vaccinia virus which has an overall Chargaff difference of only 0 086 i e only one in 1162 bases does not have a

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-jtb99-bf1.html (2012-11-26)
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  • JTheoBio,99,Bell
    transcription direction and gene location For W rich genomes the mRNA synonymous strand contains regions which if extruded from negatively supercoiled DNA would fold to generate stem loop structures with A rich loops Similarly for S rich genomes the loops would be G rich We suggest that the disposition of genes in nucleic acid sequences arises from their having to adapt to a preexisting mosaic of genomic regions each distinguished

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-jtb99-bf2.html (2012-11-26)
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  • MolBio&Evol,99,Bradnam
    remain though as to the origin nature significance and generality of this variation We conducted an extensive analysis of the yeast genome to try to answer these questions Our results indicate that open reading frames ORFs with similar G C contents at silent codon positions are significantly clustered on chromosomes This clustering can be explained by very short range correlations of silent site G C contents at neighboring ORFs ORFs

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-mbe99-b.html (2012-11-26)
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  • Gene,99,Frontali
    Gene 232 87 95 1999 Abstract A method is presented which allows detection of a sequence correlation effect not related to patchiness in base composition or to preferences in codon usage Recurrence plots providing local views of oligonucleotide recurrence regimen show that introns and intergenic regions are often characterised by a highly recurrent use of oligonucleotides By window analysis it is possible to score a long sequence for the recurrence

    Original URL path: http://linkage.rockefeller.edu/dnacorr/l-gene99-fp.html (2012-11-26)
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