TITLE:
Characterization of the sequence spectrum of DNA based on the appearance frequency of the nucleotide sequences of the genome——A new method for analysis of genome structure
AUTHORS:
Masatoshi Nakahara, Masaharu Takeda
KEYWORDS:
Appearance Frequency of Triplet in Genome Base Sequence; Self-Similarity; Analytical Method of Genome Structure
JOURNAL NAME:
Journal of Biomedical Science and Engineering,
Vol.3 No.4,
April
28,
2010
ABSTRACT: The nucleotide (base) sequence of the genome might reflect biological information beyond the coding sequences. The appearance frequencies of successive base sequences (key sequences) were calculated for entire genomes. Based on the appearance frequency of the key sequences of the genome, any DNA sequences on the genome could be expressed as a sequence spectrum with the adjoining base sequences, which could be used to study the corresponding biological phenomena. In this paper, we used 64 successive three- base sequences (triplets) as the key sequences, and determined and compared the spectra of specific genes to the chromosome, or specific genes to tRNA genes in Saccharomyces cerevisiae, Schizosaccharomyces pombe and Escherichia coli. Based on these analyses, a gene and its corresponding position on the chromosome showed highly similar spectra with the same fold enlargement (approximately 400-fold) in the S. cerevisiae, S. pombe and E. coli genomes. In addition, the homologous structure of genes that encode proteins was also observed with appropriate tRNA gene(s) in the genome. This analytical method might faithfully reflect the encoded biological information, that is, the conservation of the base sequences was to make sense the conservation of the translated amino acids sequence in the coding region, and might be universally applicable to other genomes, even those that consisted of multiple chromosomes.