title: On the origin of three base periodicity in genomes.
abstract: Genomes of almost all organisms have been found to exhibit several periodicities, the most prominent one is the three base periodicity. It is more pronounced in the gene coding regions and has been exploited to identify the segments of a genome that code for a protein. The reason for this three base periodicity in the gene-coding region has been attributed to inhomogeneous nucleotide compositions in the three codon positions. However, this reason cannot explain the three base periodicity present at the level of the whole genome where the codon concept is not applicable. Even though the distribution of each nucleotide is uniform at the positions 0(mod 3), 1(mod 3) and 2(mod 3) when the whole genome data is considered, our analysis reveals that the three base periodicity is arising because of higher correlations among the nucleotides separated by three bases.
authors.affiliation: School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India. atmabodha@gmail.com
authors.forename: Kushal
authors.initials: K
authors.lastname: Shah
authors.forename: Annangarachari
authors.initials: A
authors.lastname: Krishnamachari
mesh_terms: D001105:Archaea / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D001482:Base Composition; D001483:Base Sequence; D018834:Chaperonin 60 / Q000235:genetics; D003062:Codon / Q000235:genetics; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D016681:Genome, Fungal; D008957:Models, Genetic; D009711:Nucleotides / Q000032:analysis*; D016008:Statistical Distributions; D015003:Yeasts / Q000235:genetics
chemical_list: D018834:Chaperonin 60; D003062:Codon; D009711:Nucleotides