C-curve: a novel 3D graphical representation of DNA sequence based on codons.

In this paper, a novel 3D graphical representation of DNA sequence based on codons is proposed. Since there is not loss of information due to overlapping and containing loops, this representation will be useful for comparison of different DNA sequences. This 3D curve will be convenient for DNA mutations comparison specially. In continues we give a numerical characterization of DNA sequences based on the new 3D curve. This characterization facilitates quantitative comparisons of similarities/dissimilarities analysis of DNA sequences based on codons.

[1]  Ahmed Sallam,et al.  A Novel Approach for the Classical Ramsey Number Problem on DNA-Based Supercomputing , 2011 .

[2]  A. Nandy GRAPHICAL ANALYSIS OF DNA SEQUENCE STRUCTURE : III. INDICATIONS OF EVOLUTIONARY DISTINCTIONS AND CHARACTERISTICS OF INTRONS AND EXONS , 1996 .

[3]  Wei Chen,et al.  Invariants of DNA sequences based on 2DD-curves. , 2006, Journal of theoretical biology.

[4]  Xiaofeng Guo,et al.  Numerical characterization of DNA sequences in a 2-D graphical representation scheme of low degeneracy , 2003 .

[5]  Ali Iranmanesh,et al.  A Novel Graphical and Numerical Representation for Analyzing DNA Sequences Based on Codons , 2012 .

[6]  Xiao Sun,et al.  TN curve: A novel 3D graphical representation of DNA sequence based on trinucleotides and its applications , 2009, Journal of Theoretical Biology.

[7]  Jun Wang,et al.  Characteristic Sequences for DNA Primary Sequence , 2002, J. Chem. Inf. Comput. Sci..

[8]  Aibing Zhang,et al.  New method for comparing DNA primary sequences based on a discrimination measure , 2010, Journal of Theoretical Biology.

[9]  Milan Randic,et al.  On the Similarity of DNA Primary Sequences , 2000, J. Chem. Inf. Comput. Sci..

[10]  M. Gates A simple way to look at DNA. , 1986, Journal of theoretical biology.

[11]  Jonas S. Almeida,et al.  Alignment-free sequence comparison-a review , 2003, Bioinform..

[12]  Ashesh Nandy,et al.  On the uniqueness of quantitative DNA difference descriptors in 2D graphical representation models , 2003 .

[13]  Chun Li,et al.  Directed graphs of DNA sequences and their numerical characterization. , 2006, Journal of theoretical biology.

[14]  Donald R Forsdyke,et al.  Calculation of folding energies of single-stranded nucleic acid sequences: conceptual issues. , 2007, Journal of theoretical biology.

[15]  Zhao-Hui Qi,et al.  New 3D graphical representation of DNA sequence based on dual nucleotides , 2007, Journal of Theoretical Biology.

[16]  S. Basak,et al.  Mathematical descriptors of DNA sequences: development and applications , 2006 .

[17]  B. Blaisdell A measure of the similarity of sets of sequences not requiring sequence alignment. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Xiao Sun,et al.  Analysis of Similarities/Dissimilarities of DNA Sequences Based on a Novel Graphical Representation , 2010 .

[19]  E. Hamori,et al.  H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences. , 1983, The Journal of biological chemistry.

[20]  A. Nandy,et al.  A new graphical representation and analysis of DNA sequence structure. I: Methodology and application to globin genes , 1994 .

[21]  Xin Wang,et al.  A 3D graphical representation of protein sequences based on the Gray code. , 2012, Journal of theoretical biology.

[22]  R Zhang,et al.  Z curves, an intutive tool for visualizing and analyzing the DNA sequences. , 1994, Journal of biomolecular structure & dynamics.

[23]  Renfa Li,et al.  A Novel Composition Coding Method of DNA Sequence and Its Application , 2012 .

[24]  Milan Randic,et al.  On A Four-Dimensional Representation of DNA Primary Sequences , 2003, J. Chem. Inf. Comput. Sci..

[25]  Tianming Wang,et al.  PNN-curve: a new 2D graphical representation of DNA sequences and its application. , 2006, Journal of theoretical biology.

[26]  Bo Liao,et al.  A 2D graphical representation of DNA sequence , 2005 .

[27]  Marc S Halfon,et al.  Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs , 2008, Genome Biology.

[28]  Bo Liao,et al.  New 2D graphical representation of DNA sequences , 2004, J. Comput. Chem..

[29]  Ren Zhang,et al.  The Z curve database: a graphic representation of genome sequences , 2003, Bioinform..

[30]  P. M. Leong,et al.  Random walk and gap plots of DNA sequences , 1995, Comput. Appl. Biosci..

[31]  L. Katz,et al.  Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life. , 2010, Systematic biology.

[32]  Zhongxi Mo,et al.  Three 3D graphical representations of DNA primary sequences based on the classifications of DNA bases and their applications , 2011, Journal of Theoretical Biology.

[33]  Milan Randic,et al.  On 3-D Graphical Representation of DNA Primary Sequences and Their Numerical Characterization , 2000, J. Chem. Inf. Comput. Sci..