A graphical representation of protein based on a novel iterated function system

Physica A: Statistical Mechanics and its Applications

Volumn 403, Issue , 2014, Pages 21-28

  Ma, Tingting ^a   Liu, Yuxin ^a   Dai, Qi ^a   Yao, Yuhua ^a   He, Ping An ^a  

^a ZHEJIANG SCI TECH UNIVERSITY   (China)

Author keywords

Correlation analysis; Fuzzy cluster analysis; Mathematical description; Physicochemical property; Similarity

Indexed keywords

CLUSTER ANALYSIS; CORRELATION METHODS; FUZZY CLUSTERING; FUZZY SETS; GRAPHIC METHODS; PHYSICOCHEMICAL PROPERTIES;

2D GRAPHICAL REPRESENTATION; CORRELATION ANALYSIS; GRAPHICAL REPRESENTATIONS; ITERATED FUNCTION SYSTEM; MATHEMATICAL DESCRIPTIONS; PHYLOGENETIC TREES; PHYSICO-CHEMICAL PROPERTIES OF AMINO ACIDS; SIMILARITY;

PROTEINS;

EID: 84894634969     PISSN: 03784371     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.physa.2014.01.067     Document Type: Article

References (33)

1. E. Hamori, and J. Ruskin H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences J. Biol. Chem. 258 1983 1318 1327 (Pubitemid 13139379)
2. H.J. Jeffrey Chaos game representation of gene structure Nucleic Acids Res. 18 1990 2163 2170
3. D. Wu, J. Roberge, D.J. Cork, B.G. Nguyen, T. Grace, Computer visualization of long genomic sequences, in: IEEE Conference 1993, pp. 308-315.
4. D. Bielinska-Waz Graphical and numerical representations of DNA sequences: statistical aspects of similarity J. Math. Chem. 49 2011 2345 2407
5. M. Randic, J. Zupan, A.T. Balaban, D. Vikic-Topic, and D. Plavsic Graphical representation of proteins Chem. Rev. 111 2011 790 862
6. M. Randic 2-D graphical representation of proteins based on virtual genetic code SAR QSAR Environ. Res. 15 2004 147 157 (Pubitemid 38641775)
7. M. Randic, D. Butina, and J. Zupan Novel 2-D graphical representation of proteins Chem. Phys. Lett. 419 2006 528 532 (Pubitemid 43220524)
8. F. Bai, and T. Wang On graphical and numerical representation of protein sequences J. Biomol. Struct. Dyn. 23 2006 537 546
9. M. Randic 2-D graphical representation of proteins based on physico-chemical properties of amino acids Chem. Phys. Lett. 444 2007 176 180 (Pubitemid 47198577)
10. Y.H. Yao, Q. Dai, C. Li, P.A. He, X.Y. Nan, and Y.Z. Zhang Analysis of similarity/dissimilarity of protein sequences Proteins 73 2008 864 871
11. J. Feng, and T.M. Wang Characterization of protein primary sequences based on partial ordering J. Theoret. Biol. 254 2008 752 755
12. S.S.T. Yau, C.L. Yu, and R. He A protein map and its application DNA Cell Biol. 27 2008 241 250 (Pubitemid 351655088)
13. C. Li, X.Q. Yu, L. Yang, X.Q. Zheng, and Z.F. Wang 3-D maps and coupling numbers for protein sequences Physica A 388 2009 1967 1972
14. Y.F. Li, G.H. Huang, B. Liao, and Z.B. Liu H-L curve, a novel 2D graphical representation of protein sequences MATCH Commun. Math. Comput. Chem. 61 2009 519 532
15. M. Randic, K. Mehulic, D. Vukicevic, T. Pisanski, D. Vikic-Topic, and D. Plavsic Graphical representation of proteins as four-color maps and their numerical characterization J. Mol. Graph. 27 2009 637 641
16. J. Wen, and Y.Y. Zhang A 2D graphical representation of protein sequence and its numerical characterization Chem. Phys. Lett. 476 2009 281 286
17. Y.H. Yao, Q. Dai, L. Li, X.Y. Nan, P.A. He, and Y.Z. Zhang Similarity/dissimilarity studies of protein sequences based on a new 2D graphical representation J. Comput. Chem. 31 2010 1045 1052
18. Z.C. Wu, X.A. Xiao, and K.C. Chou 2D-MH: a web-server for generating graphic representation of protein sequences based on the physicochemical properties of their constituent amino acids J. Theoret. Biol. 267 2010 29 34
19. M.I.A. el Maaty, M.M. Abo-Elkhier, and M.A. Abd Elwahaab 3D graphical representation of protein sequences and their statistical characterization Physica A 389 2010 4668 4676
20. P.A. He, Y.P. Zhang, Y.H. Yao, Y.F. Tang, and X.Y. Nan The graphical representation of protein sequences based on the physicochemical properties and its applications J. Comput. Chem. 31 2010 2136 2142
21. J.F. Yu, X. Sun, and J.H. Wang A novel 2D graphical representation of protein sequence based on individual amino acid Int. J. Quantum Chem. 111 2011 2835 2843
22. P.A. He, X.F. Li, J.L. Yang, and J. Wang A novel descriptor for protein similarity analysis MATCH Commun. Math. Comput. Chem. 65 2011 445 458
23. B. Liao, B.Y. Liao, X.G. Lu, and Z. Cao A novel graphical representation of protein sequences and its application J. Comput. Chem. 32 2011 2539 2544
24. A. Ghosh, and A. Nandy Graphical representation and mathematical characterization of protein sequences and applications to viral proteins Adv. Protein Chem. Str. 83 2011 1 42
25. P.A. He, J.Z. Wei, Y.H. Yao, and Z.X. Tie A novel graphical representation of proteins and its application Physica A 391 2012 93 99
26. H.J. Yu, and D.S. Huang Novel graphical representation of genome sequence and its applications in similarity analysis Physica A 391 2012 6128 6136
27. M. Randic, M. Novic, A.R. Choudhury, and D. Plavsic On graphical representation of trans-membrane proteins SAR QSAR Environ. Res. 23 2012 327 343
28. P.A. He, D. Li, Y.P. Zhang, X. Wang, and Y.H. Yao A 3D graphical representation of protein sequences based on the gray code J. Theoret. Biol. 304 2012 81 87
29. H.J. Yu, and D.S. Huang Novel 20-D descriptors of protein sequences and it's applications in similarity analysis Chem. Phys. Lett. 531 2012 261 266
30. Z.H. Qi, J. Feng, X.Q. Qi, and L. Li Application of 2D graphic representation of protein sequence based on Huffman tree method Comput. Biol. Med. 42 2012 556 563
31. L. Huang, H.L. Tan, and B. Liao HR-curve: a novel 2D graphical representation of protein sequence and its multi-application J. Comput. Theor. Nanos. 10 2013 257 264
32. B. Liao, X. Shan, W. Zhu, and R. Li Phylogenetic tree construction based on 2D graphical representation Chem. Phys. Lett. 422 2006 282 288
33. M. Randic Very efficient search for protein alignment - VESPA J. Comput. Chem. 33 2012 702 707