The 5′-3′ distance of RNA secondary structures

Journal of Computational Biology

Volumn 19, Issue 7, 2012, Pages 867-878

  Han, Hillary S W ^a   Reidys, Christian M ^a  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

distance; noncrossing diagram; RNA secondary structure; singularity analysis

Indexed keywords

RNA;

ALGORITHM; ARTICLE; CHEMISTRY; CONFORMATION; ENTROPY; THEORETICAL MODEL; THERMODYNAMICS;

ALGORITHMS; ENTROPY; MODELS, THEORETICAL; NUCLEIC ACID CONFORMATION; RNA; THERMODYNAMICS;

EID: 84863887000     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2011.0301     Document Type: Article

References (16)

1. Chen, W.Y.C., Qin, J., and Reidys, C.M. 2008. Crossings and nestings of tangled diagrams. Elec. J. Comb. 15, 86.
2. Chen, W.Y.C., Deng, E.Y.P., Du, R.R.X., et al. 2007. Crossings and nestings of matchings and partitions. Trans. Am. Math. Soc. 359, 1555-1575.
3. Flajolet, P., Fill, J.A., and Kapur, N. 2005. Singularity analysis, hadamard products, and tree recurrences. J. Comput. Appl. Math. 174, 271-313. (Pubitemid 40046851)
4. Flajolet, P., and Sedgewick, R. 2009. Analytic Combinatorics. Cambridge University Press, New York.
5. Fontana, W., Konings, D.A.M., and Stadler, P.F. 1993. Statistics of RNA secondary structures. Biopolymers 33, 1389-1404. (Pubitemid 23249156)
6. Howell, J.A., Smith, T.F., and Waterman, M.S. 1980. Computation of generating functions for biological molecules. SIAM J. Appl. Math. 39, 119-133.
7. Jin, E.Y., Qin, J., and Reidys, C.M. 2008. Combinatorics of RNA structures with pseudoknots. Bull. Math. Biol. 70, 45-67.
8. Jin, E.Y., and Reidys, C.M. 2010a. Irreducibility in RNA structures. Bull. Math. Biol. 72, 375-399.
9. Jin, E.Y., and Reidys, C.M. 2010b. On the decomposition of k-noncrossing RNA structures. Adv. Appl. Math. 44, 53-70.
10. Penner, R.C., and Waterman, M.S. 1993. Spaces of RNA secondary structures. Adv. Math. 101, 31-49.
11. Reidys, C.M. 2011. Combinatorial Computational Biology of RNA. Springer-Verlag, New York.
12. Stanley, R.P. 1980. Differentiably finite power series. Eur. J. Comb. 1, 175-188.
13. Waterman, M.S. 1978. Secondary structure of single-stranded nucleic acids. Adv. Math. (Suppl. Studies) 1, 167-212.
14. Waterman, M.S. 1979. Combinatorics of RNA hairpins and cloverleafs. Stud. Appl. Math. 60, 91-96.
15. Waterman, M.S., and Schmitt, W.R. 1994. Linear trees and RNA secondary structure. Discr. Appl. Math. 51, 317-323.
16. Yoffe, A.M., Prinsen, P., Gelbart, W.M., et al. 2011. The ends of a large RNA molecule are necessarily close. Nucleic Acids Res. 39, 292-299.