A new adjacent pair 2D graphical representation of DNA sequences

Journal of Biological Systems

Volumn 21, Issue 1, 2013, Pages

  Gupta, Manoj Kumar ^a   Niyogi, Rajdeep ^a   Misra, Manoj ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY ROORKEE   (India)

Author keywords

Alignment free method; Dual nucleotide; Phylogenetic tree; Sequence similarity

Indexed keywords

EID: 84873325769     PISSN: 02183390     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0218339013500058     Document Type: Article

References (21)

1. Liao B, A 2D graphical representation of DNA sequence, Chem Phys Lett 401:196- 199, 2005.
2. Wang J, Zhang Y, Characterization and similarity analysis of DNA sequences grounded on a 2-D graphical representation, Chem Phys Lett 423:50-53, 2006.
3. Zhang Y, Liao B, Ding K, On 2D graphical representation of DNA sequence of nondegeneracy, Chem Phys Lett 411:28-32, 2005. (Pubitemid 41013956)
4. Liao B, Ding K, A 3D graphical representation of DNA sequences and its application, Theor Comput Sci 358:56-64, 2006. (Pubitemid 44088583)
5. Yuan C, Liao B, Wang T-M, New 3D graphical representation of DNA sequences and their numerical characterization, Chem Phys Lett 379:412-417, 2003.
6. Yau SS-T, Wang J, Niknejad A, Lu C, Jin N, Ho YK, DNA sequence representation without degeneracy, Nucleic Acids Res 31:3078-3080, 2003. (Pubitemid 37441767)
7. Yu C, Liang Q, Yin C, He RL, Yau SS-T, A novel construction of genome space with biological geometry, DNA Res 17:155-168, 2010.
8. Hall BG, Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences, Mol Biol Evol 22:792-802, 2005. (Pubitemid 40299529)
9. Liu XQ, Dai Q, Xiu Z, Wang T, PNN-curve: A new 2D graphical representation of DNA sequences and its application, J Theor Biol 243:555-561, 2006. (Pubitemid 44711962)
10. Qi Z, Qi X, Novel 2D graphical representation of DNA sequence based on dual nucleotides, Chem Phys Lett 440:139-144, 2007. (Pubitemid 46693718)
11. Randi'c M, Condensed representation of DNA primary sequences, J Chem Inf Comput Sci 40:50-56, 2000.
12. Wu Y, Wee-Chung Liew A, Yan H, Yang M, DB-Curve: A novel 2D method of DNA sequence visualization and representation, Chem Phys Lett 367:170-176, 2003.
13. Vinga S, Almeida J, Alignment-free sequence comparison - A review, Bioinformatics 19:513-523, 2003. (Pubitemid 36336518)
14. Yau SS-T, Yu C, He R, A protein map and its application, DNA Cell Biol 27:241-250, 2008. (Pubitemid 351655088)
15. Yu C, Deng M, Yau SS-T, DNA sequence comparison by a novel probabilistic method, Inf Sci 181:1484-1492, 2011.
16. Gupta M, Niyogi R, Misra M, An experimental analysis of phylogenetic trees based on topological score, Int Conf Information Systems Design and Intelligent Applications (INDIA 2012), Springer, Visakhapatnam, India, January 5-7, 2012, pp. 237-244.
17. Kumar S, Nei M, Dudley J, Tamura K, MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences, Brief Bioinform 9:299-306, 2008. (Pubitemid 351890826)
18. Qi X, Wu Q, Zhang Y, Fuller E, Zhang C-Q, A novel model for DNA sequence similarity analysis based on graph theory, Evol Bioinform 7:149-158, 2011.
19. Hall BG, Simulating DNA coding sequence evolution with EvolveAGene 3, Mol Biol Evol 25:688-695, 2008. (Pubitemid 351398322)
20. Rambaut A, Grass NC, Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees, Bioinformatics 13:235-238, 1997. (Pubitemid 27249927)
21. Stoye J, Evers D, Meyer F, Rose: Generating sequence families, Bioinformatics 14:157-163, 1998. (Pubitemid 28395875)