Shape-based barrier estimation for RNAs

GCB 2010 - German Conference on Bioinformatics 2010

Volumn , Issue , 2010, Pages 41-50

  Bogomolov, Sergiy ^a   Mann, Martin ^a   Voß, Björn ^a   Podelski, Andreas ^a   Backofen, Rolf ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BARRIER HEIGHTS; CELLULAR PROCESS; CONFORMATIONAL CHANGE; ENERGY PEAKS; METAHEURISTIC; OPTIMAL ESTIMATIONS; REFOLDING; REFOLDING PATHWAYS; RNA MOLECULES; SHAPE BASED;

BIOINFORMATICS; COMPUTATIONAL COMPLEXITY; CONFORMATIONS; HEURISTIC ALGORITHMS; HEURISTIC METHODS; MOLECULES; RNA;

ESTIMATION;

EID: 84871238810     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (26)

1. P.E. Black. Metaheuristic. In Dictionary of Algorithms and Data Structures. Paul E. Black, ed., U.S. National Institute of Standards and Technology, 30 March 2009. (accessed 15.06.2010) Available from: http://www.itl.nist.gov/div897/sqg/dads/HTML/metaheuristic.html.
2. P. Clote, E. Kranakis, D. Krizanc, and B. Salvy. Asymptotics of canonical and saturated RNA secondary structures. JBCB, 7(5):869-893, 2009.
3. I. Dotu, W.A. Lorenz, P. Van Hentenryck, and P. Clote. Computing folding pathways between RNA secondary structures. NAR, 38(5):1711-1722, 2010.
4. C. Flamm, W. Fontana, I.L. Hofacker, and P. Schuster. RNA folding at elementary step resolution. RNA, 6(03):325-338, 2000.
5. C. Flamm, I.L. Hofacker, S. Maurer-Stroh, P.F. Stadler, and M. Zehl. Design of multistable RNAmolecules. RNA, 7(02):254-265, 2001.
6. C. Flamm, I.L. Hofacker, P.F. Stadler, and M.T.Wolfinger. Barrier Trees of Degenerate Landscapes. Z. Phys. Chem., 216(2/2002):155-173, 2002.
7. R.W. Floyd. Algorithm 97: Shortest path. Commun. ACM, 5(6):345, 1962.
8. M. Geis, C. Flamm, M.T. Wolfinger, A. Tanzer, I.L. Hofacker, M. Middendorf, C. Mandl, P.F. Stadler, and C. Thurner. Folding kinetics of large RNAs. J of Mol Biol., 379(1):160-173, 2008.
9. R. Giegerich, B. Voss, and M. Rehmsmeier. Abstract shapes of RNA. NAR, 32(16):4843-4851, 2004.
10. I.L. Hofacker. Vienna RNA secondary structure server. NAR, 31(13):3429-31, 2003.
11. K.H. Hoffmann and P. Sibani. Diffusion in hierarchies. Phys. Rev. A, 38(8):4261-4270, 1988.
12. M. Kubota and M. Hagiya. Minimum basin algorithm: An effective analysis technique for DNA energy landscapes. LNCS, 3384:202-214, 2005.
13. K.A. LeCuyer and D.M. Crothers. The Leptomonas collosoma spliced leader RNA can switch between two alternate structural forms. Biochemistry, 32(20):53015311, 1993.
14. R. Lorenz, C. Flamm, and I.L. Hofacker. 2D projections of RNA folding landscapes. In Proc. of GCB'09, volume 157 of LNCS, pages 11-20, 2009.
15. W.A. Lorenz, Y. Ponty, and P. Clote. Asymptotics of RNA shapes. J of Comp. Biol., 15(1):31-63, 2008.
16. S.R. Morgan and P.G. Higgs. Barrier heights between ground states in a model of RNA secondary structure. J of Physics A, 31:3153-3170, 1998.
17. J. Ma?nuch, C. Thachuk, L. Stacho, and A. Condon. NP-Completeness of the Direct Energy Barrier Problem without Pseudoknots. In DNA Computing, volume 5877 of LNCS, pages 106-115, 2009.
18. M. Mann, S. Will, and R. Backofen. The Energy Landscape Library-a platform for generic algorithms. Proc. of BIRD, 7:83-86, 2007.
19. Markus Nebel and Anika Scheid. On quantitative effects of RNA shape abstraction. Theory in Biosciences, 128(4):211-225, 2009.
20. P.F. Stadler. Fitness landscapes. In LNP, pages 183-204. Springer, 2002.
21. P. Sibani, R. van der Pas, and J.C. Schon. The lid method for exhaustive exploration of metastable states of complex systems. Comp. Phys. Comm., 116(1):17-27, 1999.
22. P. Steffen, B. Voss, M. Rehmsmeier, J. Reeder, and R. Giegerich. RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics, 22(4):500-503, 2006.
23. T. Takeda, H. Ono, K. Sadakane, and M. Yamashita. A Local Search Based Barrier Height Estimation Algorithm for DNA Molecular Transitions. In DNA Computing, volume 3892 of LNCS, pages 359-370, 2006.
24. S. Wright. The Roles of Mutation. In Congress on Genetics, page 365, 1932.
25. M.T. Wolfinger, W.A. Svrcek-Seiler, C. Flamm, I.L. Hofacker, and P.F. Stadler. Efficient computation of RNA folding dynamics. J of Physics A, 37(17):4731-4741, 2004.
26. M. Zuker and P. Stiegler. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. NAR, 9(1):133-148, 1981.