ArticleNucleic acids research2011
Visualization of the protein-coding regions with a self adaptive spectral rotation approach.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- Identification of a circular code periodicity in the bacterial ribosome: origin of codon periodicity in genes?RNA biology · 2020Article
- Categorical spectral analysis of periodicity in human and viral genomes.Nucleic acids research · 2013Article
- An approach for searching insertions in bacterial genes leading to the phase shift of triplet periodicity.Genomics, proteomics & bioinformatics · 2011Article
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2 authors.
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Abstract
Identifying protein-coding regions in DNA sequences is an active issue in computational biology. In this study, we present a self adaptive spectral rotation (SASR) approach, which visualizes coding regions in DNA sequences, based on investigation of the Triplet Periodicity property, without any preceding training process. It is proposed to help with the rough coding regions prediction when there is no extra information for the training required by other outstanding methods. In this approach, at each position in the DNA sequence, a Fourier spectrum is calculated from the posterior subsequence. Following the spectrums, a random walk in complex plane is generated as the SASR's graphic output. Applications of the SASR on real DNA data show that patterns in the graphic output reveal locations of the coding regions and the frame shifts between them: arcs indicate coding regions, stable points indicate non-coding regions and corners' shapes reveal frame shifts. Tests on genomic data set from Saccharomyces Cerevisiae reveal that the graphic patterns for coding and non-coding regions differ to a great extent, so that the coding regions can be visually distinguished. Meanwhile, a time cost test shows that the SASR can be easily implemented with the computational complexity of O(N).
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