title: Representation of DNA sequences in genetic codon context with applications in exon and intron prediction.
abstract: To apply digital signal processing (DSP) methods to analyze DNA sequences, the sequences first must be specially mapped into numerical sequences. Thus, effective numerical mappings of DNA sequences play key roles in the effectiveness of DSP-based methods such as exon prediction. Despite numerous mappings of symbolic DNA sequences to numerical series, the existing mapping methods do not include the genetic coding features of DNA sequences. We present a novel numerical representation of DNA sequences using genetic codon context (GCC) in which the numerical values are optimized by simulation annealing to maximize the 3-periodicity signal to noise ratio (SNR). The optimized GCC representation is then applied in exon and intron prediction by Short-Time Fourier Transform (STFT) approach. The results show the GCC method enhances the SNR values of exon sequences and thus increases the accuracy of predicting protein coding regions in genomes compared with the commonly used 4D binary representation. In addition, this study offers a novel way to reveal specific features of DNA sequences by optimizing numerical mappings of symbolic DNA sequences.
authors.affiliation: Department of Mathematics, Statistics and Computer Science, The University of Illinois at Chicago, IL 60607-7045, USA.
authors.forename: Changchuan
authors.initials: C
authors.lastname: Yin
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D003062:Codon / Q000235:genetics*; D019295:Computational Biology; D004247:DNA / Q000235:genetics*; D030561:Databases, Nucleic Acid / Q000706:statistics & numerical data; D005091:Exons; D005583:Fourier Analysis; D005815:Genetic Code; D006801:Humans; D007438:Introns; D009010:Monte Carlo Method; D016366:Open Reading Frames; D017422:Sequence Analysis, DNA / Q000706:statistics & numerical data*; D012815:Signal Processing, Computer-Assisted; D059629:Signal-To-Noise Ratio
chemical_list: D003062:Codon; D004247:DNA
keywords: Fourier transform; Gene; exon; genetic codon; intron