3D graphical representation of protein sequences and their statistical characterization

Based on three physicochemical properties of amino acid side chains, we proposed a novel unique 3D graphical representation of protein sequences. Then, we constructed two vectors of three components as mathematical objects to characterize protein sequences numerically. The similarity/dissimilarity analysis among nine ND5 protein sequences proved the utility of our approach. A correlation and significance analysis have been provided to compare our results and the sequence homology.

[1]  Chun-Ting Zhang,et al.  A graphic representation of protein sequence and predicting the subcellular locations of prokaryotic proteins. , 2002, The international journal of biochemistry & cell biology.

[2]  Zu-Guo Yu,et al.  Chaos game representation of protein sequences based on the detailed HP model and their multifractal and correlation analyses. , 2004, Journal of theoretical biology.

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

[4]  Rodney M. J. Cotterill,et al.  Biophysics : An Introduction , 2002 .

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

[6]  François-Joseph Lapointe,et al.  A weighted least-squares approach for inferring phylogenies from incomplete distance matrices , 2004, Bioinform..

[7]  Bo Liao,et al.  Analysis of similarity/dissimilarity of DNA sequences based on 3-D graphical representation , 2004 .

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

[9]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

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

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

[12]  Xin Chen,et al.  An information-based sequence distance and its application to whole mitochondrial genome phylogeny , 2001, Bioinform..

[13]  Alexandru T. Balaban,et al.  Unique graphical representation of protein sequences based on nucleotide triplet codons , 2004 .

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

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

[16]  Humberto González-Díaz,et al.  Novel 2D maps and coupling numbers for protein sequences. The first QSAR study of polygalacturonases; isolation and prediction of a novel sequence from Psidium guajava L. , 2006, FEBS letters.

[17]  A. C. May,et al.  Percent sequence identity; the need to be explicit. , 2004, Structure.

[18]  Amir Niknejad,et al.  DNA sequence representation without degeneracy. , 2003, Nucleic acids research.

[19]  C. Zhang,et al.  A graphic approach to analyzing codon usage in 1562 Escherichia coli protein coding sequences. , 1994, Journal of molecular biology.

[20]  EUGENE HAMORI,et al.  Novel DNA sequence representations , 1985, Nature.

[21]  Khalid Sayood,et al.  A new sequence distance measure for phylogenetic tree construction , 2003, Bioinform..

[22]  Liu Yang,et al.  3-D maps and coupling numbers for protein sequences , 2009 .

[23]  Alan Wee-Chung Liew,et al.  DB-Curve: a novel 2D method of DNA sequence visualization and representation , 2003 .

[24]  P. Echenique.  Introduction to protein folding for physicists , 2007, 0705.1845.

[25]  Yu-dong Cai,et al.  Support vector machines for predicting rRNA-, RNA-, and DNA-binding proteins from amino acid sequence. , 2003, Biochimica et biophysica acta.

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

[27]  Milan Randić,et al.  2-D Graphical representation of proteins based on physico-chemical properties of amino acids , 2007 .

[28]  G D Rose,et al.  Modeling unfolded states of peptides and proteins. , 1995, Biochemistry.

[29]  Milan Randic,et al.  A novel 2-D graphical representation of DNA sequences of low degeneracy , 2001 .

[30]  Yu-hua Yao,et al.  Analysis of similarity/dissimilarity of DNA sequences based on a 3-D graphical representation , 2005 .

[31]  Jia Wen,et al.  A 2D graphical representation of protein sequence and its numerical characterization , 2009 .