Detection of Periodicity in Eukaryotic Genomes on the Basis of Power Spectrum Analysis

Atsushi Fukushima[1] (a-fukusi@bs.aist-nara.ac.jp)
Toshimichi Ikemura[2] (tikemura@lab.nig.ac.jp\\)
Taku Oshima[3] (taku@bs.aist-nara.ac.jp)
Hirotada Mori[3] (hmori@gtc.aist-nara.ac.jp)
Shigehiko Kanaya[4] (skanaya@gtc.aist-nara.ac.jp)

[1]Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan
[2]Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics; Division of Genetics, Department of Biological Science, The Graduate University for Advanced Studies, Mishima, Shizuoka 411-8540, Japan
[3]Research and Education Center for Genetic Information, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan
[4]Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0101, Japan


Abstract

In the present study, we identified periodic patterns in nucleotide sequence, and characterized nucleotide sequences that confer periodicities to Arabidopsis thaliana and Drosophila melanogaster on the basis of a power spectrum method and frequency of nucleotide sequences. To assign regions that contribute to each periodicity we calculated periodic nucleotide distributions by a parameter proposed in the paper. In A. thaliana, we obtained three periodicities (248 bp-, 167 bp-, and 126 bp) in chromosome 3, three peaks (174 bp-, 88 bp-, and 59 bp-period) in chromosome 4, and four periodicities (356 bp, 174 bp, 88 bp, and 59 bp) in chromosome 5. These are relation to ORF that consists of Gly-rich amino acid sequences including histone protein that consists of Gly-, Ser-, and Ala-rich amino acids residues. For D. melanogaster genome we found that G or C spectral curves have flat region at middle frequency range from f = 10-4 to 10-5 (corresponding to cyclic size 1 kb - 5 kb), which may be associated with randomness of base sequence composition. This property has not been observed in Saccharomyces cerevisiae, Caenorhabditis elegans, and Homo sapiens yet.

[ Full-text PDF | Table of Contents ]


Japanese Society for Bioinformatics