Bibliographic References

[1]

  S.H. Bernhart, H. Tafer, U. Mückstein, C. Flamm, P.F. Stadler, and I.L. Hofacker. Partition function and base pairing probabilities of RNA heterodimers. Algorithms for Molecular Biology, 1(1):3, 2006.

[2]

  S.H. Bernhart, I.L. Hofacker, S. Will, A.R. Gruber, and P.F. Stadler. RNAalifold: Improved consensus structure prediction for RNA alignments. BMC bioinformatics, 9(1):474, 2008.

[3]

  W. Fontana, P.F. Stadler, E.G. Bornberg-Bauer, T. Griesmacher, I.L. Hofacker, M. Tacker, P. Tarazona, E.D. Weinberger, and P. Schuster. RNA folding and combinatory landscapes. Physical review E, 47(3):2083, 1993.

[4]

  I.L. Hofacker and P.F. Stadler. Memory efficient folding algorithms for circular RNA secondary structures. Bioinformatics, 22(10):1172–1176, 2006.

[5]

  I.L. Hofacker, W. Fontana, P.F. Stadler, L.S. Bonhoeffer, M. Tacker, and P. Schuster. Fast folding and comparison of RNA secondary structures. Monatshefte für Chemie/Chemical Monthly, 125(2):167–188, 1994.

[6]

  I.L. Hofacker, M. Fekete, and P.F. Stadler. Secondary structure prediction for aligned RNA sequences. Journal of molecular biology, 319(5):1059–1066, 2002.

[7]

  Ronny Lorenz, Christoph Flamm, and Ivo L. Hofacker. 2d projections of RNA folding landscapes. In Ivo Grosse, Steffen Neumann, Stefan Posch, Falk Schreiber, and Peter F. Stadler, editors, German Conference on Bioinformatics 2009, volume 157 of Lecture Notes in Informatics, pages 11–20, Bonn, September 2009. Gesellschaft f. Informatik.

[8]

  Ronny Lorenz, Stephan H. Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F. Stadler, and Ivo L. Hofacker. ViennaRNA package 2.0. Algorithms for Molecular Biology, 6(1):26, 2011.

[9]

  D.H. Mathews, M.D. Disney, J.L. Childs, S.J. Schroeder, M. Zuker, and D.H. Turner. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proceedings of the National Academy of Sciences of the United States of America, 101(19):7287, 2004.

[10]

  J.S. McCaskill. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers, 29(6-7):1105–1119, 1990.

[11]

  B.A. Shapiro and K. Zhang. Comparing multiple RNA secondary structures using tree comparisons. Computer applications in the biosciences: CABIOS, 6(4):309–318, 1990.

[12]

  B.A. Shapiro. An algorithm for comparing multiple RNA secondary structures. Computer applications in the biosciences: CABIOS, 4(3):387–393, 1988.

[13]

  D.H. Turner and D.H. Mathews. NNDB: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. Nucleic Acids Research, 38(suppl 1):D280–D282, 2010.

[14]

  M. Zuker and P. Stiegler. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic acids research, 9(1):133–148, 1981.