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Tuyển tập báo cáo các nghiên cứu khoa học quốc tế ngành hóa học dành cho các bạn yêu hóa học tham khảo đề tài: Analysis of Free Energy Signals Arising from Nucleotide Hybridization between rRNA and mRNA Sequences during Translation in Eubacteria | Hindawi Publishing Corporation EURASIP Journal on Bioinformatics and Systems Biology Volume 2006 Article ID23613 Pages 1-9 DOI 10.1155 BSB 2006 23613 Analysis of Free Energy Signals Arising from Nucleotide Hybridization between rRNA and mRNA Sequences during Translation in Eubacteria Lalit Ponnala 1 Anne-Marie Stomp 2 Donald L. Bitzer 3 and Mladen A. Vouk3 1 Department of Electrical and Computer Engineering North Carolina State University Raleigh NC 27695 USA 2 Department of Forestry North Carolina State University Raleigh NC 27695 USA 3 Department of Computer Science North Carolina State University Raleigh NC 27695 USA Received 14 April 2006 Revised 20 September 2006 Accepted 3 October 2006 Recommended for Publication by Yidong Chen A decoding algorithm that mechanistically models the progressive alignments that arise as the mRNA moves past the rRNA tail during translation elongation is tested. Each of these alignments provides an opportunity for hybridization between the singlestranded 3-terminal nucleotides of the 16S rRNA and the spatially accessible window of mRNA sequence from which a free energy value can be calculated. Using this algorithm we show that a periodic energetic pattern of frequency 1 3 is revealed. This periodic signal exists in the majority of coding regions of eubacterial genes but not in the noncoding regions encoding the 16S and 23S rRNAs. Signal analysis reveals that the population of coding regions of each bacterial species has a mean phase that is correlatedin a statistically significant way with species G C content. These results suggest that the periodic signal could function as a synchronization signal for the maintenance of reading frame and that codon usage provides a mechanism for manipulation of signal phase. Copyright 2006 Lalit Ponnala et al. 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 .