Localizing triplet periodicity in DNA and cDNA sequences

Background: The protein-coding regions (coding exons) of a DNA sequence exhibit a triplet periodicity (TP) due to fact that coding exons contain a series of three nucleotide codons that encode specific amino acid residues. Such periodicity is usually not observed in introns and intergenic regions. If a DNA sequence is divided into small segments and a Fourier Transform is applied on each segment, a strong peak at frequency 1/3 is typically observed in the Fourier spectrum of coding segments, but not in non-coding regions. This property has been used in identifying the locations of protein-coding genes in unannotated sequence. The method is fast and requires no training. However, the need to compute the Fourier Transform across a segment (window) of arbitrary size affects the accuracy with which one can localize TP boundaries. Here, we report a technique that provides higherresolution identification of these boundaries, and use the technique to explore the biological correlates of TP r...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Liya Wang, Lincoln D. Stein
• Keywords: BMCBI 2010, Fourier Transform, TP Boundaries, Tp Region