Similarity analysis of RNA secondary structures based on 4D representation

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Volumn 56, Issue 2, 2006, Pages 249-259

  Gao, Jianwei ^a   Zhang, Xingping ^a  

^a NORTH CHINA ELECTRIC POWER UNIVERSITY   (China)

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EID: 33846345431     PISSN: 03406253     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (24)

1. C. B. E. M. Reusken, F. B. John, Structural elements of the 3′-terminal coat protein binding site in alfalfa mosaic virus RNAs, Nucleic Acids Res. 14 (1996) 2660-2665.
2. M. Randic, M. Vracko, N. Lers, D. Plavsic, Analysis of similarity/dissimilarity of DNA sequences based on novel 2-D graphical representation, Chem. Phys. Lett. 371 (2003) 202-207.
3. M. Randic, M. Vracko, On the similarity of DNA primary sequences, J. Chem. Inf. Comput. Sci. 40 (2000) 599-606.
4. M. Randic, Condensed representation of DNA primary sequences, J. Chem. Inf. Comput. Sci. 40 (2000) 50-56.
5. C. X. Yuan, B. Liao, T. M. Wang, New 3-D graphical representation of DNA sequences and their numerical characterization, Chem. Phys. Lett. 379 (2003) 412-417.
6. B. Liao, T. M. Wang, Analysis of similarity/dissimilarity of DNA sequences based on 3-D graphical representation, Chem. Phys. Lett. 388 (2004) 195-200.
7. B. Liao, T. M. Wang, Analysis of similarity of DNA sequences based on triplets, J. Chem. Inf. Comput. Sci. 44 (2004) 1666-1670.
8. B. Liao, K. Q. Ding, A graphical approach to analyzing DNA sequences, J. Comput. Chem. 26 (2005) 1519-1523.
9. B. Liao, Y. S Liu, R. F. Li, W. Zhu, Coronavirus phylogeny based on triplets of nucleic acids bases, Chem. Phys. Lett. 421 (2006) 313318.
10. B. Liao, M. S. Tan, K. Q. Ding, Application of 2D graphical representation of DNA sequence, Chem. Phys. Lett. 414 (2005) 296-300.
11. B. Liao, T. M. Wang, General combinatorics of RNA hairpins and cloverleaves, J. Chem. Inf. Comput. Sci. 43 (2003) 1138-1142.
12. B. Liao, T. M. Wang, A 3D Graphical representation of RNA secondary structures, J. Biomol. Struct. Dynamics 21 (2004) 827-832.
13. B. Liao, K. Q. Ding, T. M. Wang, On a six-dimensional representation of RNA secondary structures. J. Biomol. Struct. Dynamics 22 (2005) 455-464.
14. B. Liao, T. M. Wang, K. Q. Ding, On a seven-dimensional representation of RNA secondary structures. Mol. Simulat. 14 (2005) 1-9.
15. W. Zhu, B. Liao, K. Q. Ding, A condensed 3D graphical representation of RNA secondary structures. J. Mol. Struct. (Theochem) 757 (2005) 193-198.
16. E. C. Koper-Zwarthotf, F. T. Bredcrode, P. Walstra, J. F. Bol, Nucleotide sequence of the 3′noncoding region of alfalfa mosaic virus RNA4 and its homology with the genomic RNAs, Nucleic Acids Res. 7 (1979) 1887-1900.
17. S. W. Scott, X. Ge, The complete nucleotide sequence of RNA 3 of citrus leaf rugose and citrus variegation ilarviruses, J. Gen. Virol. 76 (1995) 957-963.
18. K. C. Koper-Zwarthoff, F. T. Bredcrode, P. Walstra, J. F. Bol, Nucleotide sequence of the putative recognition site for coat protein in the RNAs of alfalfa mosaic virus and tobacco streak virus. Nucleic Acids Res. 8 (1980) 3307-3318.
19. B. J. C. Cornelissen, H. Janssen, D. Znidema, J. F. Bol, Complete nucleotide sequence of tobacco streak virus RNA 3, Nucleic Acids Res. 12 (1984) 2427-2437.
20. R. H. Alrefai, P. J. Shiel, L. L. Domier, C. J. D'Arcy, P. H. Berger, S. S. Korban, The nucleotide sequence of apple mosaic virus coat protein gene has no similarity with other Bromoviridae coat protein genes, J. Gen. Virol. 75 (1994) 2847-2850.
21. S. W. Scott, X. Ge, The complete nucleotide sequence of the RNA 3 of lilac ring mottle ilarvirus, J. Gen. Virol. 76 (1995) 1801-1806.
22. E. J. Bachman, S. W. Scott, G. Xin, V. V. Bowman, Complete nucleotide sequence of prune dwarf viral RNA 3: Implications for coat protein activation of genome replication in ilarviruses, Virology 201 (1994) 127-131.
23. F. Houser-Scott, M. L. Baer, K. F. Liem, J. M. Cai, L. Gehrke, Nucleotide sequence and structural determinants of specific binding of coat protein or coat protein peptides to the 3′ untranslated region of alfalfa mosaic virus RNA 4, J. Virol. 68 (1994) 2194-2205.
24. EMBL/GenBank/DDBJ databases. Accession no. X86352.