Classification of RNA secondary structures using the techniques of cluster analysis

Journal of Theoretical Biology

Volumn 183, Issue 1, 1996, Pages 105-117

  Nakaya, Akihiro ^a   Yonezawa, Akinori ^a   Yamamoto, Kenji ^b  

^a UNIVERSITY OF TOKYO   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ARTICLE; CLUSTER ANALYSIS; POLIOMYELITIS VIRUS; PRIORITY JOURNAL; RNA SEQUENCE; RNA STRUCTURE; VIROID;

COCONUT CADANG-CADANG VIROID; POLIO VIRUS; POLIOVIRUS; POTATO SPINDLE TUBER VIROID; SOLANUM TUBEROSUM; VIROIDS;

EID: 0030574258     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1006/jtbi.1996.0206     Document Type: Article

References (20)

1. AKIYAMA, Y. & FURUYA, T. (1992). Folding of large RNA sequence using a Hopfield-type neural network. In: IEICE Technical Report NC90-62, The Institute of Electrical Information and Communication Engineering of Japan (in Japanese).
2. BRANLANT, C., KROL, A. & EBEL, J. P. (1981). The conformation of chicken, rat and human U1 A RNAs in solution. Nucl. Acids Res. 9, 841-857.
3. DUMAS, J.-P. & NININO, J. (1982). Efficient algorithm for folding and computing nucleic acid sequences. Nucl. Acids Res. 10, 197-206.
4. EDELBROOK, C. & MCLAUGHLIN, B. (1980). Hierarchical cluster analysis of intraclass correlations: a mixture model study. Multivariate Behav. Res. 15, 299-318.
5. FUJITANI, Y. & YAMAMOTO, K. (1994). Influence of slight sequence changes on the free energy of a single stranded ribonucleic acids molecule. J. theor. biol. 171, 151-161.
6. HASELOFF, J. & GERLACH, W. L. (1988). Simple RNA enzymes with new and highly specific endoribonuclease activities. Nature 334, 585-591.
7. HUBERT, L. J. (1974a). Some application of graph theory to clustering. Psychometrika 39, 283-309.
8. HUBERT, L. J. (1974b). Approximate evaluation techniques for the single-link and complete-link hierarchical clustering procedures. J. Am. Stat. Assoc. 69, 698-704.
9. ISHIKAWA, M., MESHI, T., OHNO, T., OKADA, Y., UEDA, I. & SHIKATA, E. (1984). A reviced replication cycle for viroids: the role of longer than unit length RNA in viroid replication. Mol. Gen. Genet. 196, 421-428.
10. JAIN, A. K. & DUBES, R. C. (1988). Algorithms for clustering data. NJ: Prentice-Hall.
11. MCCASKILL, J. S. (1990). The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29, 1105-1119.
12. MILLIGAN, G. W. & ISAAC, P. D. (1980). The validation of four ultrametric clustering algorithms. Pattern Recognition 12, 41-51.
13. MILLIGAN, G. W., SOON, S. C. & SOKOL, L. M. (1983). The effect of cluster size, dimensionality, and the number of clusters on recovery of true cluster structure. IEEE Transaction on Pattern Analysis and Machine Intelligence 5, 40-47.
14. MILLIGAN, G. W. & COOPER, M. C. (1985). An examination of procedures for determining the number of clusters in a data set. Psychometrika 50, 159-179.
15. NAKAYA, A., YAMAMOTO, K. & YONEZAWA, A. (1995). RNA secondary structure prediction using highly parallel computers. Comput. Applic. Biosci. 11, 685-692.
16. YAMAMOTO, K., KITAMURA, Y. & YOSHIKURA, H. (1984). Computation of statistical secondary structure of nucleic acids. Nucl. Acids Res. 12, 335-346.
17. YAMAMOTO, K. & YOSHIKURA, H. (1985). Computer program for prediction of the optimal and suboptimal secondary structure of long RNA molecules. Comput. Applic. Biosci. 1, 89-94.
18. YAMAMOTO, K. & YOSHIKURA, H. (1987). An improved algorithm for the prediction of optimum and suboptimum folding structures of long single-stranded RNA. Comput. Applic. Biosci. 3, 31-35.
19. ZUCKER, M. & STEIGLER, P. (1980). Optimal computer folding of large RNA sequence using thermodynamics and auxiliary information. Nucl. Acids Res. 9, 133-148.
20. ZUCKER, M. (1989). On finding all suboptimal folding of an RNA molecule. Science 244, 48-52.