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Journal of Biomedicine and Biotechnology
Volume 2005, Issue 2, Pages 139-146
http://dx.doi.org/10.1155/JBB.2005.139
Research article

Protein Coding Sequence Identification by Simultaneously Characterizing the Periodic and Random Features of DNA Sequences

1Department of Electrical & Computer Engineering, University of Florida, Gainesville 32611-6200, FL, USA
2Department of Biomedical Engineering, Whitaker Institute, Johns Hopkins University, Baltimore 21205, MD, USA
3BioSieve, 1026 Springfield Drive, Campbell 95008, CA, USA
4National Center for Atmospheric Research, Boulder 80307-3000, CO, USA

Received 24 May 2004; Revised 30 August 2004; Accepted 3 September 2004

Copyright © 2005 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Citations to this Article [34 citations]

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  • Changchuan Yin, and Stephen S.-T. Yau, “Prediction of protein coding regions by the 3-base periodicity analysis of a DNA sequence,” Journal of Theoretical Biology, vol. 247, no. 4, pp. 687–694, 2007. View at Publisher · View at Google Scholar
  • Jianbo Gao, Yinhe Cao, Wen-wen Tung, and Jing Hupp. 1–352, 2007. View at Publisher · View at Google Scholar
  • F.E. Frenkel, and E.V. Korotkov, “Classification analysis of triplet periodicity in protein-coding regions of genes,” Gene, vol. 421, no. 1-2, pp. 52–60, 2008. View at Publisher · View at Google Scholar
  • F. E. Frenkel, and E. V. Korotkov, “Classification of triplet periodicity in the DNA sequences of genes from KEGG databank,” Molecular Biology, vol. 42, no. 4, pp. 629–640, 2008. View at Publisher · View at Google Scholar
  • Nidhal Bouaynaya, and Dan Schonfeld, “Nonstationary analysis of coding and noncoding regions in nucleotide sequences,” IEEE Journal on Selected Topics in Signal Processing, vol. 2, no. 3, pp. 357–364, 2008. View at Publisher · View at Google Scholar
  • Vladimir Paar, Nenad Pavin, Ivan Basar, Marija Rosandić, Matko Glunčić, and Nils Paar, “Hierarchical structure of cascade of primary and secondary periodicities in Fourier power spectrum of alphoid higher order repeats,” BMC Bioinformatics, vol. 9, 2008. View at Publisher · View at Google Scholar
  • Е.В. Коротков, and E.V. Korotkov, “Phase Shifts of the Triplet Periodicity in DNA Sequences of Genes,” Mathematical Biology and Bioinformatics, vol. 4, no. 2, pp. 66–80, 2009. View at Publisher · View at Google Scholar
  • Frenkel, and Korotkov, “Using triplet periodicity of nucleotide sequences for finding potential reading frame shifts in genes,” DNA Research, vol. 16, no. 2, pp. 105–114, 2009. View at Publisher · View at Google Scholar
  • Chuanhua Xing, Donald L. Bitzer, Winser E. Alexander, Mladen A. Vouk, and Anne-Marie Stomp, “Identification of protein-coding sequences using the hybridization of 18S rRNA and mRNA during translation,” Nucleic Acids Research, vol. 37, no. 2, pp. 591–601, 2009. View at Publisher · View at Google Scholar
  • B. Chen, and P. Ji, “Visualization of the protein-coding regions with a self adaptive spectral rotation approach,” Nucleic Acids Research, vol. 39, no. 1, pp. e3–e3, 2010. View at Publisher · View at Google Scholar
  • Yong-chun Zuo, and Qian-zhong Li, “The hidden physical codes for modulating the prokaryotic transcription initiation,” Physica A: Statistical Mechanics and its Applications, vol. 389, no. 19, pp. 4217–4223, 2010. View at Publisher · View at Google Scholar
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  • Miriam CS Nunes, Elizabeth F Wanner, and Gerald Weber, “Origin of multiple periodicities in the Fourier power spectra of the Plasmodium falciparum genome,” BMC Genomics, vol. 12, no. Suppl4, pp. S4, 2011. View at Publisher · View at Google Scholar
  • Bo Chen, and Ping Ji, “Predicting coding region candidates in the DNA sequence based on visualization without training,” IEEE SSCI 2011 - Symposium Series on Computational Intelligence - CIBCB 2011: 2011 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pp. 1–6, 2011. View at Publisher · View at Google Scholar
  • В.М. Пугачева, and V.M. Pugacheva, “Searching Pair Points of Triplet Periodicity Phase Shifts in the Genes of 17 Bacterial Genomes,” Mathematical Biology and Bioinformatics, vol. 7, no. 2, pp. 461–475, 2012. View at Publisher · View at Google Scholar
  • Jianfeng Shao, Xiaohua Yan, and Shuo Shao, “SNR of DNA sequences mapped by general affine transformations of the indicator sequences,” Journal of Mathematical Biology, 2012. View at Publisher · View at Google Scholar
  • Bo Chen, and Ping Ji, “Numericalization of the self adaptive spectral rotation method for coding region prediction,” Journal of Theoretical Biology, vol. 296, pp. 95–102, 2012. View at Publisher · View at Google Scholar
  • Yulia M. Suvorova, Valentina M. Rudenko, and Eugene V. Korotkov, “Detection change points of triplet periodicity of gene,” Gene, vol. 491, no. 1, pp. 58–64, 2012. View at Publisher · View at Google Scholar
  • Jianbo Gao, “Complex systems and emergence: How theory meets reality,” Advances in Mechanics, vol. 43, no. 4, pp. 359–389, 2013. View at Publisher · View at Google Scholar
  • Suping Deng, Liyun Yuan, Guohui Ding, Kanyan Feng, and Yixue Li, “A new approach for identifying protein-coding regions by combining chirp z and wavelet transform,” Current Bioinformatics, vol. 8, no. 5, pp. 557–563, 2013. View at Publisher · View at Google Scholar
  • Xiaomo Yu, Junke Ye, Jing Hu, Xiaoping Liao, and Jianbo Gao, “Fractal Behavior in the Clarification Process of Cane Sugar Production,” Mathematical Problems in Engineering, vol. 2013, pp. 1–9, 2013. View at Publisher · View at Google Scholar
  • Jianbo Gao, Erik B. Lasch, and Qian Chen, “Multiscale analysis to facilitate joint chaos and fractal analysis of biosignals,” National Aerospace and Electronics Conference, Proceedings of the IEEE, pp. 96–102, 2013. View at Publisher · View at Google Scholar
  • Jianbo Gao, Qian Chen, and Erik Blasch, “Image denoising in the presence of non-Gaussian, power-law noise,” National Aerospace and Electronics Conference, Proceedings of the IEEE, pp. 103–108, 2013. View at Publisher · View at Google Scholar
  • Chen Bo, “An improved random-walk approach for visualizing periodicities hidden in biological sequences,” Processing of 2014 International Conference on Multisensor Fusion and Information Integration for Intelligent Systems, MFI 2014, 2014. View at Publisher · View at Google Scholar
  • Bo Chen, and Ping Ji, “An Exploration of the Triplet Periodicity in Nucleotide Sequences with a Mature Self-Adaptive Spectral Rotation Approach,” Journal of Applied Mathematics, vol. 2014, pp. 1–9, 2014. View at Publisher · View at Google Scholar
  • Yulia M. Suvorova, and Eugene V. Korotkov, “Study of triplet periodicity differences inside and between genomes,” Statistical Applications In Genetics And Molecular Biology, vol. 14, no. 2, pp. 113–123, 2015. View at Publisher · View at Google Scholar
  • David Velasco, Pedro Seoane, and M. Gonzalo Claros, “Bioinformatics Analyses to Separate Species Specific mRNAs from Unknown Sequences in de novo Assembled Transcriptomes,” Bioinformatics and Biomedical Engineering, vol. 9044, pp. 322–332, 2015. View at Publisher · View at Google Scholar
  • Praveen Kumar Vesapogu, Changchuan Yin, Bapi Raju Surampudi, Praveen Kumar Vesapogu, Changchuan Yin, and Bapi Raju Surampudi, “Predicting Protein Coding Regions by Six-Base Nucleotide Distribution,” Proceedings Of The Fifth International Conference On Fuzzy And Neuro Computing (Fancco - 2015), vol. 415, pp. 151–161, 2015. View at Publisher · View at Google Scholar
  • Hai-Long Hu, and Hui-Lan Fang, “The box fractal sets based on bilinear transformation iterated function system,” International Journal of Information and Communication Technology, vol. 10, no. 4, pp. 365–375, 2017. View at Publisher · View at Google Scholar
  • Jianbo Gao, Peng Fang, and Lihua Yuan, “Analyses of geographical observations in the Heihe River Basin: Perspectives from complexity theory,” Journal of Geographical Sciences, vol. 29, no. 9, pp. 1441–1461, 2019. View at Publisher · View at Google Scholar
  • Yulia M. Suvorova, and Eugene V. Korotkov, “New Method for Potential Fusions Detection in Protein-Coding Sequences,” Journal of Computational Biology, 2019. View at Publisher · View at Google Scholar
  • Y M Suvorova, M A Korotkova, K G Skryabin, and E V Korotkov, “ Search for potential reading frameshifts in cds from Arabidopsis thaliana and other genomes ,” DNA Research, 2019. View at Publisher · View at Google Scholar
  • Blake Hewelt, Haiqing Li, Mohit Kumar Jolly, Prakash Kulkarni, Isa Mambetsariev, and Ravi Salgia, “The DNA walk and its demonstration of deterministic chaos—relevance to genomic alterations in lung cancer,” Bioinformatics, 2019. View at Publisher · View at Google Scholar