Spectral-dynamic representation of DNA sequences

A graphical representation of DNA sequences in which the distribution of a particular base B=A,C,G,T is represented by a set of discrete lines has been formulated. The methodology of this approach has been borrowed from two areas of physics: spectroscopy and dynamics. Consequently, the set of discrete lines is referred to as the B-spectrum. Next, the B-spectrum is transformed to a rigid body composed of material points. In this way a dynamic representation of the DNA sequence has been obtained. The centers of mass of these rigid bodies, divided by their moments of inertia, have been taken as the descriptors of the spectra and, thus, of the DNA sequences. The performance of this method on a standard set of data commonly applied by authors introducing new approaches to bioinformatics (the first exons of β-globin genes of different species) proved to be very good.

[1]  P ? ? ? ? ? ? ? % ? ? ? ? , 1991 .

[2]  H. J. Jeffrey.  Chaos game representation of gene structure. , 1990, Nucleic acids research.

[3]  M Novic,et al.  Novel numerical and graphical representation of DNA sequences and proteins , 2006, SAR and QSAR in environmental research.

[4]  M. Novič,et al.  Spectral representation of reduced protein models , 2009, SAR and QSAR in environmental research.

[5]  Tianming Wang,et al.  A novel 2D graphical representation of DNA sequences and its application. , 2006, Journal of molecular graphics & modelling.

[6]  Qilin Xiang,et al.  A new graphical coding of DNA sequence and its similarity calculation , 2013 .

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

[8]  Milan Randic,et al.  Algorithm for Coding DNA Sequences into "Spectrum-like" and "Zigzag" Representations , 2005, J. Chem. Inf. Model..

[9]  Bo Liao,et al.  A graphical method to construct a phylogenetic tree , 2006 .

[10]  Jitender Verma,et al.  3D-QSAR in drug design--a review. , 2010, Current topics in medicinal chemistry.

[11]  Guohua Huang,et al.  H–L curve: A novel 2D graphical representation for DNA sequences , 2008 .

[12]  H. J. Jeffrey.  Chaos game representation of gene structure. , 1990, Nucleic acids research.

[13]  Kequan Ding,et al.  Novel 4D numerical representation of DNA sequences , 2005 .

[14]  C. Munteanu,et al.  Generalized lattice graphs for 2D-visualization of biological information , 2009, Journal of Theoretical Biology.

[15]  Dejan Plavšić,et al.  Novel spectral representation of RNA secondary structure without loss of information , 2009 .

[16]  Dejan Plavšić,et al.  Milestones in graphical bioinformatics , 2013 .

[17]  Dejan Plavšić,et al.  A novel unexpected use of a graphical representation of DNA : Graphical alignment of DNA sequences , 2006 .

[18]  M. Randic,et al.  2-D Graphical representation of proteins based on virtual genetic code , 2004, SAR and QSAR in environmental research.

[19]  Maykel Cruz-Monteagudo,et al.  3D-MEDNEs: an alternative "in silico" technique for chemical research in toxicology. 2. quantitative proteome-toxicity relationships (QPTR) based on mass spectrum spiral entropy. , 2008, Chemical research in toxicology.

[20]  Guohua Huang,et al.  Similarity studies of DNA sequences based on a new 2D graphical representation. , 2009, Biophysical chemistry.

[21]  Wieslaw Nowak,et al.  Distribution moments of 2D-graphs as descriptors of DNA sequences , 2007 .

[22]  S. Vilar,et al.  A network-QSAR model for prediction of genetic-component biomarkers in human colorectal cancer. , 2009, Journal of theoretical biology.

[23]  Ali Iranmanesh,et al.  3D-Dynamic Representation of DNA Sequences , 2012 .

[24]  Ali Iranmanesh,et al.  C-curve: a novel 3D graphical representation of DNA sequence based on codons. , 2013, Mathematical biosciences.

[25]  Y. Liu,et al.  A novel technique for analyzing the similarity and dissimilarity of DNA sequences. , 2014, Genetics and molecular research : GMR.

[26]  Remigijus Didziapetris,et al.  In silico technology for identification of potentially toxic compounds in drug discovery , 2006 .

[27]  Xinguo Lu,et al.  A novel graphical representation of protein sequences and its application , 2011, J. Comput. Chem..

[28]  D. Bieli.  Moments of Inertia of Spectra and Distribution Moments as Molecular Descriptors , 2013 .

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

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

[31]  Shankar Subramaniam,et al.  Classification studies based on a spectral representation of DNA. , 2010, Journal of theoretical biology.

[32]  Dejan Plavšić,et al.  Analysis of similarity/dissimilarity of DNA sequences based on novel 2-D graphical representation , 2003 .

[33]  D. Bielinska-Waz,et al.  2D-dynamic representation of DNA sequences as a graphical tool in bioinformatics , 2016 .

[34]  Bo Liao,et al.  Phylogenetic tree construction based on 2D graphical representation , 2006 .

[35]  Cristian Robert Munteanu,et al.  Alignment-free prediction of mycobacterial DNA promoters based on pseudo-folding lattice network or star-graph topological indices , 2008, Journal of Theoretical Biology.

[36]  Wen Zhu,et al.  A 2D graphical representation of DNA sequence based on dual nucleotides and its application , 2009 .

[37]  Dhundy Bastola,et al.  Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis , 2014, Briefings Bioinform..

[38]  D. Bielinska-Waz,et al.  Non-standard similarity/dissimilarity analysis of DNA sequences. , 2014, Genomics.

[39]  Milan Randić.  Spectrum-like graphical representation of DNA based on codons , 2006 .

[40]  Jie Song.  A new 3-D graphical representation of DNA sequences and their numerical characterization , 2009, 2009 4th International Conference on Computer Science & Education.

[41]  Lourdes Santana,et al.  Scoring function for DNA–drug docking of anticancer and antiparasitic compounds based on spectral moments of 2D lattice graphs for molecular dynamics trajectories , 2009, European Journal of Medicinal Chemistry.

[42]  Tao Song,et al.  ColorSquare: A Colorful Square Visualization of DNA Sequences , 2012 .

[43]  Chun Li,et al.  Analysis of similarity/dissimilarity of protein sequences , 2008, Proteins.

[44]  Dorota Bielińska-Wa̧ż.  Four-component spectral representation of DNA sequences , 2009 .

[45]  Tianming Wang,et al.  Linear regression model of short k-word: a similarity distance suitable for biological sequences with various lengths. , 2013, Journal of theoretical biology.

[46]  Milan Randic.  Very efficient search for protein alignment—VESPA , 2012, J. Comput. Chem..

[47]  Piotr Waz,et al.  Similarity studies of DNA sequences using genetic methods , 2007 .

[48]  D. Bielinska-Waz.  Graphical and numerical representations of DNA sequences: statistical aspects of similarity , 2011, Journal of mathematical chemistry.

[49]  Milan Randic.  Very efficient search for nucleotide alignments , 2013, J. Comput. Chem..

[50]  Renfa Li,et al.  Coronavirus phylogeny based on triplets of nucleic acids bases , 2006, Chemical Physics Letters.

[51]  Humberto González Díaz,et al.  Comparative Study of Topological Indices of Macro/Supramolecular RNA Complex Networks , 2008, J. Chem. Inf. Model..

[52]  Wenbing Hou,et al.  A new graphical representation of protein sequences and its applications , 2016 .

[53]  S. Basak,et al.  2D-dynamic representation of DNA/RNA sequences as a characterization tool of the zika virus genome , 2017 .

[54]  Ping-an He,et al.  A novel descriptor of protein sequences and its application. , 2014, Journal of theoretical biology.

[55]  P. He,et al.  A novel graphical representation of proteins and its application , 2012 .

[56]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[57]  Milan Randić.  On a geometry-based approach to protein sequence alignment , 2008 .

[58]  Wen Zhu,et al.  A Numerical Representation of DNA Sequences and Its Applications , 2008 .

[59]  Jure Zupan,et al.  Novel 2-D graphical representation of proteins , 2006 .

[60]  Kuo-Chen Chou,et al.  HP-Lattice QSAR for dynein proteins: experimental proteomics (2D-electrophoresis, mass spectrometry) and theoretic study of a Leishmania infantum sequence. , 2008, Bioorganic & medicinal chemistry.

[61]  Renfa Li,et al.  A group of 3D graphical representation of DNA sequences based on dual nucleotides , 2008 .

[62]  Timothy Clark,et al.  2D-dynamic representation of DNA sequences , 2007 .

[63]  Guillermín Agüero-Chapín,et al.  QSAR for RNases and theoretic–experimental study of molecular diversity on peptide mass fingerprints of a new Leishmania infantum protein , 2009, Molecular Diversity.

[64]  Xuyu Xiang,et al.  Coronavirus phylogeny based on 2D graphical representation of DNA sequence , 2006, J. Comput. Chem..

[65]  Tomaz Pisanski,et al.  Protein alignment: Exact versus approximate. An illustration , 2015, J. Comput. Chem..

[66]  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.

[67]  Bo Liao and Wen Zhu.  Analysis of Similarity/Dissimilarity of DNA Primary Sequences Based on Condensed Matrices and Information Entropies , 2006 .

[68]  A. Iranmanesh,et al.  Spider representation of DNA sequences , 2014 .

[69]  Alexandru T Balaban,et al.  Graphical representation of proteins. , 2011, Chemical reviews.

[70]  Bo Liao,et al.  A 3D graphical representation of DNA sequences and its application , 2006, Theor. Comput. Sci..

[71]  Piotr Wąż,et al.  Descriptors of 2D-dynamic graphs as a classification tool of DNA sequences , 2013, Journal of Mathematical Chemistry.

[72]  Tian-ming Wang,et al.  Related matrices of DNA primary sequences based on triplets of nucleic acid bases , 2006 .

[73]  Humberto González Díaz,et al.  QSAR model for alignment‐free prediction of human breast cancer biomarkers based on electrostatic potentials of protein pseudofolding HP‐lattice networks , 2008, J. Comput. Chem..

[74]  Fionn Murtagh,et al.  Ward’s Hierarchical Agglomerative Clustering Method: Which Algorithms Implement Ward’s Criterion? , 2011, Journal of Classification.

[75]  Jure Zupan,et al.  On representation of proteins by star-like graphs. , 2007, Journal of molecular graphics & modelling.

[76]  Dejan Plavšić,et al.  Novel 2-D graphical representation of DNA sequences and their numerical characterization , 2003 .

[77]  Bo Liao,et al.  Analysis of Similarity / Dissimilarity of DNA Sequences Based on Dual Nucleotides , .

[78]  D. Bielinska-Waz,et al.  20D-dynamic representation of protein sequences. , 2016, Genomics.

[79]  Changchuan Yin,et al.  A Novel Method for Comparative Analysis of DNA Sequences by Ramanujan-Fourier Transform , 2014, J. Comput. Biol..