Genome Informatics
Online ISSN : 2185-842X
Print ISSN : 0919-9454
ISSN-L : 0919-9454
Detection of Periodicity in Eukaryotic Genomes on the Basis of Power Spectrum Analysis
Atsushi FukushimaToshimichi IkemuraTaku OshimaHirotada MoriShigehiko Kanaya
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JOURNAL FREE ACCESS

2002 Volume 13 Pages 21-29

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Abstract

In the present study, we identified periodic patterns in nucleotide sequence, and characterizednucleotide 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.

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© Japanese Society for Bioinformatics
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