title: Self-similar mitochondrial DNA.
abstract: We show that repeated sequences, like palindromes (local repetitions) and homologies between two different nucleotide sequences (motifs along the genome), compose a self-similar (fractal) pattern in mitochondrial DNA. This self-similarity comes from the looplike structures distributed along the genome. The looplike structures generate scaling laws in a pseudorandom DNA walk constructed from the sequence, called a Lévy flight. We measure the scaling laws from the generalized fractal dimension and singularity spectrum for mitochondrial DNA walks for 35 different species. In particular, we report characteristic loop distributions for mammal mitochondrial genomes.
authors.affiliation: Institute of Physics, University of São Paulo, São Paulo, Brazil and Department of Physics, University of Notre Dame, Notre Dame, IN, USA. oiwa@fge.if.usp.br
authors.forename: Nestor N
authors.initials: NN
authors.lastname: Oiwa
authors.forename: James A
authors.initials: JA
authors.lastname: Glazier
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D000818:Animals; D001483:Base Sequence; D001703:Biophysics / Q000379:methods*; D004272:DNA, Mitochondrial / Q000235:genetics / Q000378:metabolism*; D019281:Dimerization; D017709:Fractals; D016678:Genome; D006801:Humans; D006860:Hydrogen Bonding; D008928:Mitochondria / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012336:RNA, Ribosomal, 16S / Q000737:chemistry
chemical_list: D004272:DNA, Mitochondrial; D012336:RNA, Ribosomal, 16S