TY - JOUR
T1 - Detecting Periodicities in Eukaryotic Genomes by Ramanujan Fourier Transform
AU - Zhao, Jian
AU - Wang, Jiasong
AU - Jiang, Hongmei
N1 - Funding Information:
We gratefully acknowledge financial support from the natural science fund for colleges and universities in Jiangsu Province of China (17KJB180005), the Natural Science Foundation of Jiangsu Province, (BK 20150935), the Sino-foreign cooperation in running a high-level demonstrative university construction, and the project development in Jiangsu Province of China (Second Batch). We sincerely appreciate the editors/ reviewers work.
PY - 2018/9
Y1 - 2018/9
N2 - Ramanujan Fourier transform (RFT) nowadays is becoming a popular signal processing method. RFT is used to detect periodicities in exons and introns of eukaryotic genomes in this article. Genomic sequences of nine species were analyzed. The highest peak in the spectrum amplitude corresponding to each exon or intron is regarded as the significant signal. Accordingly, the periodicity corresponding to the significant signal can be also regarded as a valuable periodicity. Exons and introns have different periodic phenomena. The computational results reveal that the 2-, 3-, 4-, and 6-base periodicities of exons and introns are four kinds of important periodicities based on RFT. It is the first time that the 2-base periodicity of introns is discovered through signal processing method. The frequencies of the 2-base periodicity and the 3-base periodicity occurrence are polar opposite between the exons and the introns. With regard to the cyclicality of the Ramanujan sums, which is the base function of the transformation, RFT is suggested for studying the periodic features of dinucleotides, trinucleotides, and q nucleotides.
AB - Ramanujan Fourier transform (RFT) nowadays is becoming a popular signal processing method. RFT is used to detect periodicities in exons and introns of eukaryotic genomes in this article. Genomic sequences of nine species were analyzed. The highest peak in the spectrum amplitude corresponding to each exon or intron is regarded as the significant signal. Accordingly, the periodicity corresponding to the significant signal can be also regarded as a valuable periodicity. Exons and introns have different periodic phenomena. The computational results reveal that the 2-, 3-, 4-, and 6-base periodicities of exons and introns are four kinds of important periodicities based on RFT. It is the first time that the 2-base periodicity of introns is discovered through signal processing method. The frequencies of the 2-base periodicity and the 3-base periodicity occurrence are polar opposite between the exons and the introns. With regard to the cyclicality of the Ramanujan sums, which is the base function of the transformation, RFT is suggested for studying the periodic features of dinucleotides, trinucleotides, and q nucleotides.
KW - 2-base periodicity
KW - 3-base periodicity
KW - Ramanujan Fourier transform
KW - modulo distribution sequence
KW - periodicity detection
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U2 - 10.1089/cmb.2017.0252
DO - 10.1089/cmb.2017.0252
M3 - Article
C2 - 29963923
AN - SCOPUS:85053214840
VL - 25
SP - 963
EP - 975
JO - Journal of Computational Biology
JF - Journal of Computational Biology
SN - 1066-5277
IS - 9
ER -