RNA pseudoknot structures with arc-length ≥ 3 and stack-length ≥ σ

Discrete Applied Mathematics

Volumn 158, Issue 1, 2010, Pages 25-36

  Jin, Emma Y ^a   Reidys, Christian M ^a  

^a NANKAI UNIVERSITY   (China)

Author keywords

Enumeration; Generating function; Pseudoknot; RNA secondary structure

Indexed keywords

ARC LENGTH; ENUMERATION; GENERATING FUNCTION; NONCROSSING; PREDICTION ALGORITHMS; PSEUDOKNOT; RNA PSEUDOKNOT STRUCTURES; RNA SECONDARY STRUCTURE; RNA STRUCTURES;

ALGORITHMS; CARBON DIOXIDE ARC WELDING; CAVITY RESONATORS; FUNCTION EVALUATION; RNA;

NUCLEIC ACIDS;

EID: 70449133438     PISSN: 0166218X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dam.2009.08.004     Document Type: Article

References (24)

1. Chamorro M., Parkin N., and Varmus H.E. An RNA pseudoknots and an optimal heptameric shift site are required for highly efficent ribosomal frameshifting on a retroviral messenger RNA. Proc. Natl. Acad. Sci. USA 89 2 (1992) 713-717
2. Chen W.Y.C., Deng E.Y.P., Du R.R.X., Stanley R.P., and Yan C.H. Crossings and nestings of matchings and partitions. Trans. Amer. Math. Soc. 359 4 (2007) 1555-1575
3. Flajolet P., and Sedgewick R. Analytic Combinatorics (2008), Cambridge University Press
4. Flamm C., Fontana W., Hofacker I.L., and Schuster P. RNA folding kinetics at elementary step resolution. RNA 6 (2000) 325-338
5. Grabiner D.J., and Magyar P. Random walks in Weyl chambers and the decomposition of tensor powers. J. Algebraic Combin. 2 (1993) 239-260
6. Haslinger C., and Stadler P.F. RNA structures with pseudo-knots. Bull. Math. Biol. 61 (1999) 437-467
7. Howell J.A., Smith T.F., and Waterman M.S. Computation of generating functions for biological molecules. SIAM J. Appl. Math. 39 (1980) 119-133
8. F.W.D. Huang, W.W.J. Peng, C.M. Reidys, Folding 3-noncrossing RNA pseudoknot structures, J. Comput. Biol., 2008 (in press)
9. Jin E.Y., Qin J., and Reidys C.M. Combinatorics of RNA structures with pseudoknots. Bull. Math. Biol. 70 1 (2008) 45-67
10. Jin E.Y., and Reidys C.M. Asymptotic enumberation of RNA structures with pseudoknots. Bull. Math. Biol. 70 4 (2008) 951-970
11. Jin E.Y., and Reidys C.M. Combinatorial design of pseudoknot RNA. Adv. Appl. Math. 42 (2009) 135-151
12. E.Y. Jin, C.M. Reidys, R. Wang, Asymptotic analysis k-noncrossing matchings, 2008. arXiv:0803.0848
13. Konings D.A.M., and Gutell R.R. A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs. RNA 1 (1995) 559-574
14. Loria A., and Pan T. Domain structure of the ribozyme from eubacterial ribonuclease P. RNA 2 (1996) 551-563
15. Odlyzko A.M. Asymptotic enumeration methods. Handbook of Combinatorics vol. 2 (1995), MIT Press 1021-1231
16. Mapping RNA form and function. Science 309 (2005) 1441-1632
17. Stanley R.P. Differentiably finite power series. European J. Combin. 1 (1980) 175-188
18. Sundaram S. The Cauchy identity for S p (2 n). J. Combin. Theory, Ser. A. 53 (1990) 209-238
19. Titchmarsh E.C. The Theory of Functions (1939), Oxford University Press, London
20. Tuerk C., MacDougal S., and Gold L. RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase. Proc. Natl. Acad. Sci. USA 89 (1992) 6988-6992
21. Waterman M.S. Secondary structure of single-stranded nucleic acids. Adv. Math. I 1 (1978) 167-212
22. Waterman M.S. Combinatorics of RNA hairpins and cloverleafs. Stud. Appl. Math. 60 (1979) 91-96
23. Waterman M.S., and Smith T.F. Rapid dynamic programming algorithms for RNA secondary structure. Adv. Appl. Math. 7 (1986) 455-464
24. Westhof E., and Jaeger L. RNA pseudoknots. Curr. Opin. Struct. Biol. 2 (1992) 327-333