A novel 2D graphical representation of DNA sequences and its application

Journal of Molecular Graphics & Modelling
Qi DaiTianming Wang

Abstract

In this paper, we introduce a novel 2D graphical representation of DNA sequences, the W-curve, which is embedded in two unit circles. We associate the W-curves with the classifications of the nucleotides according to their chemical properties. Then we obtain an 8-component vector with entries being the average sums of the abscissa and y-axis of A+C and T+G (A+T and C+G, A+G and T+C), respectively. The introduced vector results in simpler characterizations and comparisons of DNA sequences. The construction of the W-curve has some important advantages: (1) it avoids loss of information and the W-curve standing for DNA doesn't overlap or intersect itself; (2) the space the W-curve occupied is very small, just two unit circles. The utility of the approach can be illustrated by the examination of similarities/dissimilarities among the coding sequences of the first exon of beta-globin gene of eleven different species in Table 1.

References

Apr 7, 1986·Journal of Theoretical Biology·M A Gates
Mar 26, 2003·Journal of Chemical Information and Computer Sciences·Milan Randić, Alexandru T Balaban

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Citations

Jan 5, 2014·EURASIP Journal on Bioinformatics & Systems Biology·Sai ZouJunfeng Wang
Sep 1, 2014·Genomics·Piotr Wąż, Dorota Bielińska-Wąż
Jan 16, 2007·Journal of Molecular Graphics & Modelling·Milan RandićDrazen Vikić-Topić
Jun 7, 2008·Proteins·Yu-Hua YaoYao-Zhou Zhang
Jan 15, 2014·Journal of Theoretical Biology·Yuhua YaoPing-an He
Mar 6, 2007·Journal of Computational Chemistry·Qi DaiDamir Vukicevic
Sep 19, 2006·Journal of Computational Chemistry·Qi DaiTian-Ming Wang
Feb 23, 2008·Journal of Computational Chemistry·Yu-Hua YaoYao-Zhou Zhang
Feb 26, 2008·Proteomics·Humberto González-DíazEugenio Uriarte
Sep 25, 2009·Journal of Computational Chemistry·Yu-Hua YaoYao-Zhou Zhang
Sep 24, 2008·Journal of Biomolecular Structure & Dynamics·Ying Guo, Tian-ming Wang
Feb 8, 2011·Journal of Biomolecular Structure & Dynamics·Xiaoqing LiuZerong He
Apr 24, 2009·Journal of Biomolecular Structure & Dynamics·Cangzhi JiaQing Yang
Nov 15, 2011·International Journal of Quantum Chemistry·Ying GuoSheng-Li Zhang
Dec 15, 2010·Journal of Biomolecular Structure & Dynamics·Guisong Chang, Tianming Wang
Feb 22, 2021·Computers in Biology and Medicine·Dorota Bielińska-Wąż, Piotr Wąż
Sep 2, 2006·Journal of Theoretical Biology·Xiao Qing LiuTianming Wang
Oct 14, 2016··P. Wa̧żD. Bielińska-Wa̧ż

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