On the analysis of large-scale genomic structures.
We apply methods from statistical physics (histograms, correlation functions, fractal dimensions, and singularity spectra) to characterize large-scale structure of the distribution of nucleotides along genomic sequences. We discuss the role of the extension of noncoding segments ("junk DNA") for the genomic organization, and the connection between the coding segment distribution and the high-eukaryotic chromatin condensation. The following sequences taken from GenBank were analyzed: complete genome of Xanthomonas campestri, complete genome of yeast, chromosome V of Caenorhabditis elegans, and human chromosome XVII around gene BRCA1. The results are compared with the random and periodic sequences and those generated by simple and generalized fractal Cantor sets.
Oiwa
Nestor Norio
NN
Instituto de Física, Universidade de São Paulo, Caixa Postal 66318, 05315-970 São Paulo, SP, Brazil. oiwa@fge.if.usp.br
Goldman
Carla
C
D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D017709:Fractals; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D016008:Statistical Distributions