ArticleGenome research2003
Gene prediction by spectral rotation measure: a new method for identifying protein-coding regions.
Article in Genome research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Optimized convolutional neural network using African vulture optimization algorithm for the detection of exons.Scientific reports · 2025Article
- DeepTSS: multi-branch convolutional neural network for transcription start site identification from CAGE data.BMC bioinformatics · 2022Article
- Prediction of Sphingosine protein-coding regions with a self adaptive spectral rotation method.PloS one · 2019Article
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- Periodic power spectrum with applications in detection of latent periodicities in DNA sequences.Journal of mathematical biology · 2016Article
- In search of coding and non-coding regions of DNA sequences based on balanced estimation of diffusion entropy.Journal of biological physics · 2016Article
- Short Exon Detection via Wavelet Transform Modulus Maxima.PloS one · 2016Article
- A new method to cluster DNA sequences using Fourier power spectrum.Journal of theoretical biology · 2015Article
- Wavelet analysis of frequency chaos game signal: a time-frequency signature of theEURASIP journal on bioinformatics & systems biology · 2014Article
- Genomic signal processing methods for computation of alignment-free distances from DNA sequences.PloS one · 2014Article
- A two-stage exon recognition model based on synergetic neural network.Computational and mathematical methods in medicine · 2014Article
- SNR of DNA sequences mapped by general affine transformations of the indicator sequences.Journal of mathematical biology · 2013Article
- Map-invariant spectral analysis for the identification of DNA periodicities.EURASIP journal on bioinformatics & systems biology · 2012Article
- Origin of multiple periodicities in the Fourier power spectra of the Plasmodium falciparum genome.BMC genomics · 2011Article
- An approach for searching insertions in bacterial genes leading to the phase shift of triplet periodicity.Genomics, proteomics & bioinformatics · 2011Article
- Visualization of the protein-coding regions with a self adaptive spectral rotation approach.Nucleic acids research · 2011Article
- Significant deviations in the configurations of homologous tandem repeats in prokaryotic genomes.Genomics, proteomics & bioinformatics · 2009Article
- Classifying coding DNA with nucleotide statistics.Bioinformatics and biology insights · 2009Article
- Identification of protein-coding sequences using the hybridization of 18S rRNA and mRNA during translation.Nucleic acids research · 2009Article
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2 authors.
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Abstract
A new measure for gene prediction in eukaryotes is presented. The measure is based on the Discrete Fourier Transform (DFT) phase at a frequency of 1/3, computed for the four binary sequences for A, T, C, and G. Analysis of all the experimental genes of S. cerevisiae revealed distribution of the phase in a bell-like curve around a central value, in all four nucleotides, whereas the distribution of the phase in the noncoding regions was found to be close to uniform. Similar findings were obtained for other organisms. Several measures based on the phase property are proposed. The measures are computed by clockwise rotation of the vectors, obtained by DFT for each analysis frame, by an angle equal to the corresponding central value. In protein coding regions, this rotation is assumed to closely align all vectors in the complex plane, thereby amplifying the magnitude of the vector sum. In noncoding regions, this operation does not significantly change this magnitude. Computing the measures with one chromosome and applying them on sequences of others reveals improved performance compared with other algorithms that use the 1/3 frequency feature, especially in short exons. The phase property is also used to find the reading frame of the sequence.
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