Biomedical Engineering Reference
In-Depth Information
References
1. Ding, Y., Lawrence, C.E.: A statistical sampling algorithm for RNA secondary structure
prediction. Nucleic Acids Research 31, 7280-7301 (2003)
2. Ding, Y., Chan, C.Y., Lawrence, C.E.: Sfold web server for statistical folding and rational
design of nucleic acids. Nucleic Acids Research 32, W135-W141 (2004)
3. McCaskill, J.S.: The equilibrium partition function and base pair binding probabilities for
RNA secondary structure. Biopolymers 29, 1105-1119 (1990)
4. Nebel, M.E., Scheid, A.: Evaluation of a sophisticated SCFG design for RNA secondary
structure prediction. Theory in Biosciences 130, 313-336 (2011)
5. Zuker, M.: On finding all suboptimal foldings of an RNA molecule. Science 244, 48-52
(1989)
6. Zuker, M.: Mfold web server for nucleic acid folding and hybridization prediction. Nucleic
Acids Res. 31, 3406-3415 (2003)
7. Hofacker, I., Fontana, W., Stadler, P., Bonhoeffer, S., Tacker, M., Schuster, P.: Fast folding
and comparison of rna secondary structures (the Vienna RNA package). Monatsh Chem. 125,
167-188 (1994)
8. Hofacker, I.L.: The vienna RNA secondary structure server. Nucleic Acids Research 31,
3429-3431 (2003)
9. Knudsen, B., Hein, J.: RNA secondary structure prediction using stochastic context-free
grammars and evolutionary history. Bioinformatics 15, 446-454 (1999)
10. Knudsen, B., Hein, J.: Pfold: RNA secondary structure prediction using stochastic context-
free grammars. Nucleic Acids Research 31, 3423-3428 (2003)
11. Wexler, Y., Zilberstein, C., Ziv-Ukelson, M.: A study of accessible motifs and RNA folding
complexity. Journal of Computational Biology 14, 856-872 (2007)
12. Backofen, R., Tsur, D., Zakov, S., Ziv-Ukelson, M.: Sparse RNA folding: Time and space
efficient algorithms. Journal of Discrete Algorithms 9, 12-31 (2011)
13. Frid, Y., Gusfield, D.: A simple, practical and complete
O ( n 3 / log( n )) -time algorithm for
RNA folding using the Four-Russians speedup. Algorithms for Molecular Biology 5, 5-13
(2010)
14. Akutsu, T.: Approximation and exact algorithms for RNA secondary structure prediction and
recognition of stochastic context-free languages. J. Comb. Optim. 3, 321-336 (1999)
15. Sprinzl, M., Horn, C., Brown, M., Ioudovitch, A., Steinberg, S.: Compilation of tRNA se-
quences and sequences of tRNA genes. Nucleic Acids Res. 26, 148-153 (1998)
16. Do, C.B., Woods, D.A., Batzoglou, S.: CONTRAfold: RNA secondary structure prediction
without physics-based models. Bioinformatics 22, e90-e98 (2006)
17. Dowell, R.D., Eddy, S.R.: Evaluation of several lightweight stochastic context-free grammars
for RNA secondary structure prediction. BMC Bioinformatics 5, 71 (2004)
18. Scheid, A.: Sampling and Approximation in the Context of RNA Secondary Structure Pre-
diction, PhD-Thesis Kaiserslautern University, Germany (2012)
Search WWH ::




Custom Search