An O(n5) algorithm for MFE prediction of kissing hairpins and 4-chains in nucleic acids

Journal of Computational Biology

Volumn 16, Issue 6, 2009, Pages 803-815

  Chen, Ho Lin ^a   Condon, Anne ^b   Jabbari, Hosna ^b  

^a California Institute of Technology   (United States)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

Kissing hairpins; Pseudoknot; RNA; Secondary structure prediction

Indexed keywords

APTAMER; NANOMATERIAL; RNA; NUCLEIC ACID;

AMINO ACID SEQUENCE; ARTICLE; ENERGY; GENETIC ALGORITHM; MATHEMATICAL PARAMETERS; NUCLEIC ACID ANALYSIS; PREDICTION; PRIORITY JOURNAL; STRUCTURE ANALYSIS; ALGORITHM; BIOLOGY; CHEMISTRY; CONFORMATION; METHODOLOGY; THERMODYNAMICS;

ALGORITHMS; APTAMERS, NUCLEOTIDE; COMPUTATIONAL BIOLOGY; NUCLEIC ACID CONFORMATION; NUCLEIC ACIDS; THERMODYNAMICS;

EID: 69249214078     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2008.0219     Document Type: Article

References (21)

1. Akutsu, T. 2000. Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots. Discrete Appl. Math. 104, 45-62.
2. Andronescu, M., Bereg, V., Hoos, H., et al. 2008. RNA STRAND: the RNA secondary structure and statistical analysis database. BMC Bioinform, 9, 340.
3. Dirks, R.M., and Pierce, N.A. 2003. A partition function algorithm for nucleic acid secondary structure including pseudoknots. J. Comput. Chem. 24, 1664-1677.
4. Dirks, R.M., and Pierce, N.A. 2004. Triggered amplification by hybridization chain reaction. Proc. Natl. Acad. Sci. USA 101, 15275-15278.
5. He, Y., Ye, T., Su, M., et al. 2008. Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra. Nature 452, 198-201.
6. Hofacker, I.L., Fontana, W., Stadler, P.F., et al. 1994. Fast folding and comparison of RNA secondary structures. Monatshefte für Chemie/Chemical Monthly 125, 167-188.
7. Lee, K., Varma, S., Santalucia, J., et al. 1997. In vivo determination of RNA structure-function relationships: analysis of the 790 loop in ribosomal RNA. J. Mol. Biol. 269, 732-743.
8. Lyngs O.R.B. 2004. Complexity of pseudoknot prediction in simple models. In Diaz, J., Karhumaki, J., Lepistö, A., and Sannella, D., eds. ICALP, Springer, Lect. Notes Comput. Sci. 3142, 919-931.
9. Lyngs O. R.B., and Pedersen, C.N. 2000. RNA pseudoknot prediction in energy-based models. J. Comput. Biol. 7, 409-427.
10. Mathews, D.H., Sabina, J., Zuker, M., et al. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288, 911-940.
11. McCaskill, J.S. 1990. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29, 1105-1119.
12. Rastegari, B., and Condon, A. 2007. Parsing nucleic acid pseudoknotted secondary structure: algorithm and applications. J. Comput. Biol. 14, 16-32.
13. Reeder, J., and Giegerich, R. 2004. Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinform. 5.
14. Rivas, E., and Eddy, S.R. 1999. A dynamic programming algorithm for RNA structure prediction including pseu-doknots. J. Mol. Biol. 285, 2053-2068.
15. Rothemund, P.W., Papadakis, N., and Winfree, E. 2004. Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biol. 2, e431.
16. Simmel, F.C., and Dittmer, W.U. 2005. DNA nanodevices. Small 1, 284-299.
17. Uemura, Y., Hasegawa, A., Kobayashi, S., et al. 1999. Tree adjoining grammars for RNA structure prediction. Theor. Comput. Sci. 210, 277-303.
18. Weinberg, Z., Regulski, E.E., Hammond, M.C., et al. 2008. The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. RNA 14, 822-828.
19. Zuker, M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406-3415.
20. Zuker, M., and Sankoff, D. 1984. RNA secondary structures and their prediction. B Math Biol. 46, 591-621.
21. Zuker, M., and Stiegler, P. 1981. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9, 133-148.