DIFFERENTIATING THE PROTEIN CODING AND NONCODING RNA SEGMENTS OF DNA USING SHANNON ENTROPY

P. Mazaheri, A. H. Shirazi, N. Saeedi, G. Reza Jafari () and Muhammad Sahimi
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P. Mazaheri: Interdisciplinary Neuroscience Research Program (INRP) — Tehran University of Medical Sciences, Tehran, Iran;
A. H. Shirazi: Interdisciplinary Neuroscience Research Program (INRP) — Tehran University of Medical Sciences, Tehran, Iran;
N. Saeedi: Interdisciplinary Neuroscience Research Program (INRP) — Tehran University of Medical Sciences, Tehran, Iran;
G. Reza Jafari: Department of Physics, Shahid Beheshti University, G. C., Evin, Tehran 19839, Iran;
Muhammad Sahimi: Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211, USA

International Journal of Modern Physics C (IJMPC), 2010, vol. 21, issue 01, 1-9

Abstract: The complexity of DNA sequences is evaluated in order to differentiate between protein-coding and noncoding RNA segments. The method is based on computing the Shannon entropy of the sequences. By comparing the entropy of the original sequence with that of its shuffled one, we identify the source of the difference between the two segments and their relative contributions to the sequence. To demonstrate the method, the DNA sequences of the bacteriumClostridium difficile 630(G + C = 29.1%)andBdellovibrio bacteriovorus(G + C = 50.6%)are analyzed, which are representatives of bacteria with unbalanced and balanced nucleotide content, respectively. It is shown that in both bacteria, regardless of nucleotide content,ΔrS— the relative difference of the two entropies — is significantly greater in protein-coding regions, when compared with noncoding RNA segments.

Keywords: DNA Sequence; Shannon Entropy (search for similar items in EconPapers)
Date: 2010
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DOI: 10.1142/S0129183110014975

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