A novel graphical and numerical representation for analyzing DNA sequences based on codons

Match

Volumn 68, Issue 2, 2012, Pages 611-620

  Jafarzadeh, Nafiseh ^a   Iranmanesh, Ali ^a  

^a TARBIAT MODARES UNIVERSITY   (Iran)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84872134670     PISSN: 03406253     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (33)

1. A. Nandy, On the uniqueness of quantitative DNA difference descriptors in 2D graphical representation models, Chem. Phys. Lett. 368 (2003) 102-107.
2. X. Guo, A. Nandy, Numerical characterization of DNA sequences in a 2-D graphical representation scheme of low degeneracy, Chem. Phys. Lett. 369 (2003) 361-366.
3. E. Hamori, 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.
4. A. Nandy, M. Harle, S. C. Basak, Mathematical descriptors of DNA sequences, ARKIVOC 9 (2006) 211-238.
5. B. Liao, T. M. Wang, New 2D graphical representation of DNA sequences, J. Comput. Chem. 25 (2004) 1364-1368.
6. B. Liao, W. Zhu, Y. Liu, 3D Graphical representation of DNA sequence without degeneracy and its applications in constructing phylogenic tree, MATCH Commun. Math. Comput. Chem. 56 (2006) 209-216.
7. B. Liao, A 2D graphical representation of DNA sequence, Chem. Phys. Lett. 401 (2005) 196-199.
8. M. Randić, M. Vračko, A. Nandy, S. C. Basak, On 3-D graphical representation of DNA primary sequences and their numerical characterization. J. Chem. Inf. Comput. Sci. 40 (2000) 1235-1244.
9. J. F. Yu, J. H.Wang, X. Sun, Analysis of similarities/dissimilarities of DNA sequences based on a novel graphical representation, MATCH Commun. Math. Comput. Chem. 63 (2010) 493-512.
10. M. Randić, A. T. Balaban, On a four-dimensional representation of DNA primary sequences. J. Chem. Inf. Comput. Sci. 43 (2003) 532-539.
11. E. Hamori, 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.
12. M. A. Gates, A simple way to look at DNA, J. Theor. Biol. 119 (1986) 319-328.
13. A. Nandy, A new graphical representation and analysis of DNA sequence structure I. Methodology and application to globin genes, Curr. Sci. 66 (1994) 309-313.
14. P. M. Leong, S. Morgenthaler, Random walk and gap plots of DNA sequences, Comput. Appl. Biosci. 11 (1995) 503-507.
15. A. Nandy, Graphical analysis of DNA sequence structure: III. Indications of evolutionary distinctions and characteristics of introns and exons, Curr. Sci. 70 (1996) 661-668.
16. R. Wu, Q. Hu, R. Li, G. Yue, A novel composition coding method of DNA sequence and its application, MATCH Commun. Math. Comput. Chem. 67 (2012) 269-276.
17. X. Zhou, K. Li, M. Goodman, A. Sallam, A novel approach for the classical Ramsey number problem on DNA-based supercomputing, MATCH Commun. Math. Comput. Chem. 66 (2011) 347-370.
18. Q. Zhang, B. Wang, On the bounds of DNA coding with H-distance, MATCH Commun. Math. Comput. Chem. 66 (2011) 371-380.
19. W. Wang, T. Wang, Conditional LZ complexity and its application in mtDNA sequence analysis, MATCH Commun. Math. Comput. Chem. 66 (2011) 425-443.
20. Q. Zhang, B. Wang, X. Wei, Evaluating the different combinatorial constraints in DNA computing based on minimum free energy, MATCH Commun. Math. Comput. Chem. 65 (2011) 291-308.
21. Y. Zhang, W. Chen, A new measure for similarity searching in DNA sequences, MATCH Commun. Math. Comput. Chem. 65 (2011) 477-488.
22. R. Wu, R. Li, B. Liao, G. Yue, A novel method for visualizing and analyzing DNA sequences, MATCH Commun. Math. Comput. Chem. 63 (2010) 679-690.
23. W. Chen, B. Liao, Y. Liu, W. Zhu, Z. Su, A numerical representation of DNA sequences and its applications, MATCH Commun. Math. Comput. Chem. 60 (2008) 291-300.
24. J. Pesek, A. Žerovnik, Numerical characterization of modified Hamori curve representation of DNA sequences, MATCH Commun. Math. Comput. Chem. 60 (2008) 301-312.
25. Y. Zhang, W. Chen, New invariant of DNA sequences, MATCH Commun. Math. Comput. Chem. 58 (2007) 197-208.
26. V. Aram, A. Iranmanesh, 3D-dynamic representation of DNA sequences, MATCH Commun. Math. Comput. Chem. 67 (2012) 809-816.
27. B. Liao, C. Zeng, F. Q. Li, Y. Tang, Analysis of similarity/dissimilarity of DNA sequences based on dual nucleotides, MATH Commun. Math. Comput. Chem. 56 (2006) 209-216.
28. C. Li, J. Wang, New invariant of DNA sequences, J. Chem. Inf. Model. 45 (2005) 115-120.
29. C. Li, N. Tang, J. Wang, Directed graphs of DNA sequences and their numerical characterization, J. Theor. Biol. 241 (2006) 173-177.
30. M. Randić, M. Vračko, On the similarity of DNA primary sequences, J. Chem. Inf. Comput. Sci. 40 (2000) 599-606.
31. M. Randić, M. Vračko, N. Lerš, D. Plavšić, Analysis of similarity/dissimilarity of DNA sequences based on novel 2-D graphical representation. Chem. Phys. Lett. 371 (2003) 202-207.
32. Y. Liu, The numerical characterization and similarity analysis of DNA primary sequences, Internet El. J. Mol. Des. 1 (2002) 675-684.
33. P. He, J. Wang, Characteristic sequences for DNA primary sequence, J. Chem. Inf. Comput. Sci. 42 (2002) 1080-1085.