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Shimizu, T., Toumoto, A., Ihara, K., Shimizu, M., Kyo-goku, Y., Ogawa, N., Oshima, Y. and Hakoshima, T. (1997) Crystal structure of PHO4 bHLH domain-DNA complex: Flanking base recognition. EMBO Journal, 16(15), 4689-4697.

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• TITLE: Identification of the interactive region by the homology of the sequence spectrum

  AUTHORS: Masatoshi Nakahara, Masaharu Takeda

  KEYWORDS: Spectrum of Genome Base Sequence; Homology of Sequence Spectrum; Interactive Region; Reverse-Complement Symmetry; Multiple Fractality; Analytical Method Of Genome

  JOURNAL NAME: Journal of Biomedical Science and Engineering, Vol.3 No.9, September 29, 2010

  ABSTRACT: The base sequence in genome was governed by some fundamental principles such as reverse-complement symmetry, multiple fractality and so on, and the analytical method of the genome structure, the “Sequence Spectrum Method (SSM)”, based on the structural features of genomic DNA faithfully visualized these principles. This paper reported that the sequence spectrum in SSM closely reflected the biological phenomena of protein and DNA, and SSM could identify the interactive region of protein-protein and DNA-protein uniformly. In order to investigate the effectiveness of SSM we analyzed the several protein-protein and DNA-protein interaction published primarily in the genome of Saccharomyces cerevisiae. The method proposed here was based on the homology of sequence spectrum, and it advantageously and surprisingly used only base sequence of genome and did not require any other information, even information about the amino-acid sequence of protein. Eventually it was concluded that the fundamental principles in genome governed not only the static base sequence but also the dynamic function of protein and DNA.