A novel method of 2D graphical representation for proteins and its application

Match

Volumn 75, Issue 2, 2016, Pages 431-446

  Sun, Dandan ^a   Xu, Chunrui ^a   Zhang, Yusen ^a  

^a SHANDONG UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84955602033     PISSN: 03406253     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (38)

1. Y. S. Zhang, W. Chen, A new measure for similarity searching in DNA sequences, MATCH Commun. Math. Comput. Chem. 65 (2011) 477-488.
2. Y. S. Zhang, W. Chen, Comparisons of RNA secondary structures based on LZ complexity, MATCH Commun. Math. Comput. Chem. 63 (2010) 513-528.
3. P. P. Qian, Y. S. Zhang, G. Q. Jian, A novel representation of protein sequences and its application, J. Converg. Inf. Tech. 6 (2011) 227-235.
4. Z. C. Wu, X. Xiao, K. C. Chou, 2D-MH: A web-server for generating graphic rep- resentation of protein sequences based on the physicochemical properties of their constituent amino acids, J. Theor. Biol. 267 (2010) 29-34.
5. Z. C. Mu, J. Wu, Y. S. Zhang, A novel method for similarity/dissimilarity analysis of protein sequences, Physica A 392 (2013) 6361-6366.
6. Y. S. Zhang, X. T. Yu, Analysis of protein sequence similarity, The Fifth International Conference on Bio-Inspired Computing: Theories and Applications, 2010, pp. 1255- 1258.
7. V. Brendel, P. Bucher, I. R. Nourbakhsh, B. E. Blaisdell, S. Karlin, Methods and algorithms for statistical analysis of protein sequences, Proc. Natl. Acad. Sci. USA 89 (1992) 2002-2006.
8. D. M. Fowler, C. L. Araya, S. J. Fleishman, E. H. Kellogg, J. J. Stephany, D. Baker ,S. Fields, High-resolution mapping of protein sequence-function relationships, Nature Meth. 7 (2010) 741-746.
9. H. Y. Wu, Y. S. Zhang, W. Chen, Z. C. Mu, Comparative analysis of protein primary sequences with graph energy, Physica A 437 (2015) 249-262.
10. H. Li, N. Homer, A survey of sequence alignment algorithms for next-generation sequencing, Brief Bioinf. 11 (2010) 473-483.
11. A. Chakraborty , S. Bandyopadhyay, FOGSAA: Fast optimal global sequence align- ment algorithm, Sci Rep. 3 (2013) #1746 (pages 9).
12. D. F. Feng, R. F. Doolittle, Progressive sequence alignment as a prerequisite to correct phylogenetic trees, J. Mol. Evol. 25 (1987) 351-360.
13. S. Vinga, J. Almeida, Alignment-free sequence comparison - review, Bioinf. 19 (2003) 513-523.
14. T. D. Pham, J. Zuegg, A probabilistic measure for alignment-free sequence compar- ison, Bioinf. 20 (2004) 3455-3461.
15. G. Reinert, D. Chew, F. Z. Sun, M. S. Waterman, Alignment-free sequence compar- ison (I): Statistics and power, J. Comput. Biol. 16 (2009) 1615-1634.
16. M. R. Kantorovitz, G. E. Robinson, S. Sinha, A statistical method for alignment-free comparison of regulatory sequences, Bioinf. 23 (2007) i249-i255.
17. I. Borozan, S. Watt, V. Ferretti, Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classiçation, Bioinf. 31 (2015) 1396-1404.
18. Y. H. Yao, Q. Dai, C. Li, P. A. He, X. Y. Nan, Y. Z. Zhang, Analysis of similar- ity/dissimilarity of protein sequences, Proteins 73 (2008) 864-871.
19. P. A. He, J. Z. Wei, Y. H. Yao, Z. X. Tie, A novel graphical representation of proteins and its application, Physica A 391 (2012) 93-99.
20. Y. H. Yao, Q. Dai, L. Li, X. Y. Nan, P. A. HE, Y. Z. Zhang, Similarity/dissimilarity studies of protein sequences based on a new 2D graphical representation, J. Comput. Chem. 31 (2010) 1045-1052.
21. A. A. Zamyatin, Protein volume in solution, Prog. Biophys. Mol. Biol. 24 (1972) 107-123.
22. C. Chotia, The nature of the accessible and buried surfaces in proteins, J. Mol. Biol. 105 (1975) 1-14.
23. C. Tandford, The interpretation of hydrogen ion titration curves of proteins, Adv. Protein Chem. 17 (1962) 70-165.
24. E. J. Cohn, J. T. Edsall, Proteins, Amino Acids and Peptides as Ions and Dipolar Ions, Reinhold Pub. Corp., New York, 1943.
25. X. H. Xia, W. H. Li, What amino acid properties affect protein evolution? J. Mol. Evol. 47 (1998) 557-564.
26. C. L. Yu, S. Y. Cheng, R. L. He, S. S. T. Yau, Protein map: An alignment-free sequence comparison method based on various properties of amino acids, Gene 486 (2011) 110-118.
27. I. Gutman, The energy of a graph, Ber. Math. Stat. Sekt. 103 (1978) 1-22.
28. S. S. T. Yau, C. L. Yu ,R. He, A protein map and its application, DNA. Cell. Biol. 27 (2008) 241-250.
29. M. A. Larkin, G. Blackshields, N. P. Brown, R. Chenna, P. A. McGettigan, H. McWilliam, F. Valentin, I. M. Wallace, A. Wilm, R. Lopez, J. D. Thompson, T. J. Gibson ,D. G. Higgins, Clustal W and Clustal X version 2.0, Bioinf. 23 (2007) 2947-2948.
30. R. Chenna, H. Sugawara, T. Koike, R. Lopez, T. J. Gibson, D. G. Higgins, J. D. Thompson, Multiple sequence alignment with the Clustal series of programs, Nucleic Acids Res. 31 (2003) 3497-3500.
31. Z. C. Mu, J. Wu , Y. S. Zhang, A novel method for similarity/dissimilarity analysis of protein sequences, Physica A 392 (2013) 6361-6366.
32. S. L. Zhang , L. P. Yang , T. M. Wang, Use of information discrepancy measure to compare protein secondary structures, J. Mol. Struct. (Theochem) 909 (2009) 102-106.
33. Y. Wang, L. Y. Wu, J. H. Zhang, Z. W. Zhan, X. S. Zhang, L. Chen, Evaluating protein similarity from coarse structures, IEEE/ACM Trans. Comput. Biol. Bioinf. 6 (2009) 583-593.
34. M. Randiç, J. Zupan, A. T. Balaban, D. Vikiç-Topiç, D. Plavsiç, Graphical repre- sentation of proteins, Chem. Rev. 111 (2011) 790-862.
35. I. Gutman, D. Vidoviç, N. Cmiljanoviç, S. Milosavljeviç, S. Radenkoviç, Graph en- ergy - A useful molecular structure-descriptor, Indian J. Chem. 42A (2003) 1309-1311.
36. I. Gutman, J. Y. Shao, The energy change of weighted graphs, Lin. Algebra Appl. 435 (2011) 2425-2431.
37. I. Gutman, Laplacian energy of a graph, Lin. Algebra Appl. 414 (2006) 29-37.
38. B. Zhou, I. Gutman, On Laplacian energy of graphs, MATCH Commun. Math. Com- put. Chem. 57 (2007) 211-220.