A 3D graphical representation of DNA sequences and its application

Theoretical Computer Science

Volumn 358, Issue 1, 2006, Pages 56-64

  Liao, Bo ^a   Ding, Kequan ^b  

^a HUNAN UNIVERSITY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Characteristic curve; DNA; Graphical representation; Phylogenic tree; Similarity

Indexed keywords

COMPUTER SCIENCE; GENES; GRAPH THEORY; INFORMATION ANALYSIS; MATHEMATICAL MODELS;

CHARACTERISTIC CURVE; GRAPHICAL REPRESENTATION; PHYLOGENIC TREE; SIMILARITY;

DNA;

EID: 33746210129     PISSN: 03043975     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tcs.2005.12.012     Document Type: Article

References (22)

1. Gates M.A. Simple DNA sequence representations. Nature 316 (1985) 219
2. Guo X., and Nandy A. Numerical characterization of DNA sequences in a 2-D graphical representation scheme of low degeneracy. Chem. Phys. Lett. 369 (2003) 361-366
3. Hamori E. Novel DNA sequence representations. Nature 314 (1985) 585-586
4. Hamori E., and Ruskin J. H curves. a novel method of representation of nucleotides series especially suited for long DNA sequences, J. Biol. Chem. 258 (1983) 1318-1327
5. He P., and Wang J. Characteristic sequences for DNA primary sequence. J. Chem. Inf. Comput. Sci. 42 (2002) 1080-1085
6. Liao B. A 2D graphical representation of DNA sequence. Chem. Phys. Lett. 401 (2005) 196-199
7. Liao B., and Wang T. New 2D graphical representation of DNA sequences. J. Comput. Chem. 25 11 (2004) 1364-1368
8. Liao B., and Wang T. 3-D Graphical representation of DNA sequences and their numerical characterization. J. Molecular Structure: THEOCHEM 681 (2004) 209-212
9. Liao B., and Wang T. Analysis of similarity of DNA sequences based on 3D graphical representation. Chem. Phys. Lett. 388 (2004) 195-200
10. Liao B., and Wang T. Analysis of similarity of DNA sequences based on triplets. J. Chem. Inf. Comput. Sci. 44 (2004) 1666-1670
11. Liao B., Zhang Y., Ding K., and Wang T. Analysis of similarity/dissimilarity of DNA sequences based on a condensed curve representation. J. Molecular Structure: THEOCHEM 717 (2005) 199-203
12. Nandy A. A new graphical representation and analysis of DNA sequence structure: I. Methodology and application to globin genes. Curr. Sci. 66 (1994) 309-314
13. Nandy A. Two-dimensional graphical representation of DNA sequences and intron-exon discrimination in intron-rich sequences. Comput. Appl. Biosci. 12 (1996) 55-62
14. Randic M. Condensed Representation of DNA Primary Sequences. J. Chem. Inf. Comput. Sci. 40 (2000) 50-56
15. Randic M., Vracko M., Lers N., and Plavsic D. Novel 2-D graphical representation of DNA sequences and their numerical characterization. Chem. Phys. Lett. 368 (2003) 1-6
16. Randic M., Vracko M., and Lers N. Dejanplavsic, Analysis of similarity/dissimilarity of DNA sequences based on novel 2-D graphical representation. Chem. Phys. Lett. 371 (2003) 202-207
17. Randic M., Vracko M., Nandy A., and Basak S.C. On 3-D graphical representation of DNA primary sequence and their numerical characterization. J. Chem. Inf. Comput. Sci. 40 (2000) 1235-1244
18. Randic M., Vracko M., Zupan J., and Novic M. Compact 2-D graphical representation of DNA. Chem. Phys. Lett. 373 (2003) 558-562
19. Raychaudhury C., and Nandy A. Indexing scheme and similarity measure for macromolecular sequences. J. Chem. Inf. Comput. Sci. 39 (1999) 243-247
20. Yan S.S.-T., Wang J., Niknejad A., Lu C., Jin N., and Ho Y.-k. DNA sequence representation without degeneracy. Nucl. Acids Res. 31 12 (2003) 3078-3080
21. Yuan C., Liao B., and Wang T. New 3-D graphical representation of DNA sequences and their numerical characterization. Chem. Phys. Lett. 379 (2003) 412-417
22. Zhang R., and Zhang C.T. Z-curve, an intuitive tool for visualizing and analyzing the DNA sequences. J. Biomol. Str. Dyn. 11 4 (1994) 767-782