Please use this identifier to cite or link to this item: http://hdl.handle.net/10397/6666
Title: Visualization of the protein-coding regions with a self adaptive spectral rotation approach
Authors: Chen, B
Ji, P 
Keywords: Eukaryotic gene prediction
Hidden-Markov-Model
DNA-sequences
Nucleotide-sequences
Triplet periodicity
Genomic sequences
Z curve
Identification
Recognition
Fourier
Issue Date: Jan-2011
Publisher: Oxford University Press
Source: Nucleic acids research, Jan. 2011, v. 39, no. 1, e3, p. 1-14 How to cite?
Journal: Nucleic acids research 
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).
URI: http://hdl.handle.net/10397/6666
ISSN: 0305-1048
EISSN: 1362-4962
DOI: 10.1093/nar/gkq891
Rights: © The Author(s) 2010. Published by Oxford University Press.
The article is available at http://dx.doi.org/10.1093/nar/gkq891
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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