A Fourier characteristic of coding sequences: origins and a non-Fourier approximation.
The 3-base periodicity, identified as a pronounced peak at the frequency N/3 (N is the length of the DNA sequence) of the Fourier power spectrum of protein coding regions, is used as a marker in gene-finding algorithms to distinguish protein coding regions (exons) and noncoding regions (introns) of genomes. In this paper, we reveal the explanation of this phenomenon which results from a nonuniform distribution of nucleotides in the three coding positions. There is a linear correlation between the nucleotide distributions in the three codon positions and the power spectrum at the frequency N/3. Furthermore, this study indicates the relationship between the length of a DNA sequence and the variance of nucleotide distributions and the average Fourier power spectrum, which is the noise signal in gene-finding methods. The results presented in this paper provide an efficient way to compute the Fourier power spectrum at N/3 and the noise signal in gene-finding methods by calculating the nucleotide distributions in the three codon positions.
Yin
Changchuan
C
Department of Mathematics, Statistics and Computer Science, The University of Illinois at Chicago, Chicago, IL 60607-7045, USA.
Yau
Stephen S-T
SS
D000818:Animals; D003062:Codon / Q000235:genetics*; D019295:Computational Biology; D004247:DNA / Q000235:genetics; D030541:Databases, Genetic; D005091:Exons; D005583:Fourier Analysis; D023281:Genomics / Q000706:statistics & numerical data; D007438:Introns; D011506:Proteins / Q000235:genetics; D013269:Stochastic Processes
D003062:Codon; D011506:Proteins; D004247:DNA