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  • corr in DNA (70s)
    of long and short repetitive sequence relations in the sea urchin genome Nucleic Acids Research 4 5 1553 1567 1976 isochore G Macaya JP Thiery G Bernardi 1976 An approach to the organization of eukaryotic genomes at a macromolecular level Journal of Molecular Biology 108 237 254 isochore JP Thiery G Macaya G Bernardi 1976 An analysis of eukaryotic genomes by density gradient centrifugation Journal of Molecular Biology 108 219

    Original URL path: http://linkage.rockefeller.edu/dnacorr/70s.html (2012-11-26)
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  • corr in DNA (60s)
    A Konberg 1961 Enzymatic synthesis of deoxyribonucleic acidsL VII Frequencies of nearest neighbor base sequences in deoxyribonucleic acid Journal of Biological Chemistry 236 864 875 N Sueoka 1961 Variation and heterogeneity of base composition of deoxyribonucleic acids a compilation of old and new data Journal of Molecular Biology 3 31 40 1962 Noboru Sueoka 1962 On the genetic basis of variation and heterogeneity of DNA base composition Proceedings of the

    Original URL path: http://linkage.rockefeller.edu/dnacorr/60s.html (2012-11-26)
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  • corr in DNA (50s)
    1991 1990 80s 70s 60s 50s about links complete genomes gene duplication dna protein music gene recognition mirror 50s 1959 R Rolfe M Meselson 1959 The relative homogeneity of microbial DNA Proceedings of the National Academy of Sciences 45 1039 1043 Noboru Sueoka 1959 A Statistical analysis of deoxyribonucleic acid distribution in density gradient centrifugation Proceedings of the National Academy of Sciences 45 10 1480 1490 PDF N Sueoka J

    Original URL path: http://linkage.rockefeller.edu/dnacorr/50s.html (2012-11-26)
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  • DNA correlations: about this bibliography
    DNA and protein sequences as fixed entities and uses various statistical methods counting is the simplest one to characterize features in the text of these sequences Sequence statistics used for predicting genes are treated in a separate bibliography http www nslij genetics org gene The dynamic category treats DNA sequences as a product of evolution and investigates which particular process led to which particular feature Although point mutation is the most studied dynamical process I m more interested in large scale duplication process To keep this focused I created a separate page on gene duplication http www nslij genetics org duplication The usual suspects topics that motivated this bibliography at the first place Large scale base composition variations heterogeneity isochore Basic properties on base composition entropy Characterizing whole sequence correlation structure correlation function traditional spectral analysis wavelet analysis Multiple scaled features fractal 1 f noise self similarity scale invariance domains within domains Other topics that this bibliography is expanding to a symmetry about strand symmetry or strand a symmetry isochore isochore large scale variation of GC content period 3 periodicity of three bases period 10 11 periodicity of ten or eleven bases repeats tandom repeats not many papers listed dna

    Original URL path: http://linkage.rockefeller.edu/dnacorr/about.html (2012-11-26)
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  • DNA correlations: links
    Donald Forsdyke Bailin Hao Hanspeter Herzel Terry Hwa Samuel Karlin 1924 2007 from Stanford Report Eugene V Korotkov Jeffrey Lawrence HC Paul Lee Wen Hsiung Li Jean Lobry Ricardo Mansilla Jose L Oliver Astero Provata Eugene Stanley Claude Thermes Edward Trifonov Jon Widom 1955 2011 from northwestern news Ken Wolfe Chun Ting Zhang Erwin Chargaff papers 1929 92 George Gamow Memorial Lecture Susumu Ohno biographical memoirs NAR 2007 database issue

    Original URL path: http://linkage.rockefeller.edu/dnacorr/links.html (2012-11-26)
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  • Preparing " datafile " for LINKAGE
    Q1 Which LINKAGE program do you want to run MLINK LINKMAP CMAP ILINK CILINK LODSCORE CLODSCORE Note MLINK calculates LOD score table it can also calculate the risk usually for two point 1 marker plus 1 trait LINKMAP CMAP performs multipoint linkage analysis for general CEPH pedigrees with fixed map distances ILINK CILINK estimates recombination fractions and max LOD score for general CEPH pedigrees LODSCORE CLODSCORE is almost identical with ILINK CILINK but for 2 groups of loci cases only Q2 How many loci Note The number of loci could include one disease locus if there is one Q3 Do you want to calculate genetic risk yes no Note you can only calculate risk for the trait locus and the person whose risk is to be calculated should have an unknown trait e g unknown affection status You will have to identify this person when you prepare pedfile using MAKEPED Q4 Are you going to use markers on X chromosome yes no Note another way to ask this question is whether the linkage analysis is sex linked Q5 Allow new mutation yes no Note it is equivalent to ask whether you allow the possibility that a disease allele is not

    Original URL path: http://linkage.rockefeller.edu/cgi-bin/webpreplink.cgi (2012-11-26)
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  • load mark
    one affectation locus describing the disease allele frequencies and penetrances Following this should be entered the information for each marker as in the following example 3 6 D1S1234 20 15 15 40 05 05 The 3 on the first line is obligatory followed by the number of alleles for the marker If desired a followed by the name of the marker may be entered and this name will then appear

    Original URL path: http://linkage.rockefeller.edu/soft/gh/loadmark.html (2012-11-26)
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  • use
    the affectation locus does not count in this numbering scheme as it does in the Linkage parameter file or by the names specified in the comment area for each marker If a map is specified in the Linkage parameter file it will be entered automatically during the load markers step Enter use without arguments to see what current linkage map has been entered IF THERE IS NO LINKAGE MAP IN

    Original URL path: http://linkage.rockefeller.edu/soft/gh/use.html (2012-11-26)
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