
\begin{DoxyEnumerate}
\item 
\end{DoxyEnumerate}

\label{mp_ref_mathews_04}
\hypertarget{mp_ref_mathews_04}{}
 D.H. Mathews, M. D. Disney, J.L. Childs, S.J. Schroeder, M. Zuker, D.H. Turner (2004)\par
 Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure, Proc Natl Acad Sci U S A, 101(19):7287-\/92
\begin{DoxyEnumerate}
\item \label{mp_ref_mathews_99}
\hypertarget{mp_ref_mathews_99}{}
 D.H. Mathews, J. Sabina, M. Zuker and H. Turner (1999)\par
 Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure, JMB, 288: 911-\/940
\item \label{mp_ref_zuker_81}
\hypertarget{mp_ref_zuker_81}{}
 Zuker and P. Stiegler (1981)\par
 Optimal computer folding of large RNA sequences using thermodynamic and auxiliary information, Nucl Acid Res 9: 133-\/148
\item \label{mp_ref_dimitrov_04}
\hypertarget{mp_ref_dimitrov_04}{}
 D.A. Dimitrov, M.Zuker(2004)\par
 Prediction of hybridization and melting for double stranded nucleic acids, Biophysical J. 87: 215-\/226,
\item \label{mp_ref_mccaskill_90}
\hypertarget{mp_ref_mccaskill_90}{}
 J.S. McCaskill (1990)\par
 The equilibrium partition function and base pair binding probabilities for RNA secondary structures, Biopolymers 29: 1105-\/1119
\item \label{mp_ref_turner_88}
\hypertarget{mp_ref_turner_88}{}
 D.H. Turner, N. Sugimoto and S.M. Freier (1988)\par
 RNA structure prediction, Ann Rev Biophys Biophys Chem 17: 167-\/192
\item \label{mp_ref_jaeger_89}
\hypertarget{mp_ref_jaeger_89}{}
 J.A. Jaeger, D.H. Turner and M. Zuker (1989)\par
 Improved predictions of secondary structures for RNA, Proc. Natl. Acad. Sci. 86: 7706-\/7710
\item \label{mp_ref_he_91}
\hypertarget{mp_ref_he_91}{}
 L. He, R. Kierzek, J. SantaLucia, A.E. Walter and D.H. Turner (1991)\par
 Nearest-\/Neighbor Parameters For GU Mismatches, Biochemistry 30: 11124-\/11132
\item \label{mp_ref_peritz_91}
\hypertarget{mp_ref_peritz_91}{}
 A.E. Peritz, R. Kierzek, N, Sugimoto, D.H. Turner (1991)\par
 Thermodynamic Study of Internal Loops in Oligoribonucleotides ... , Biochemistry 30: 6428-\/-\/6435
\item \label{mp_ref_walter_94}
\hypertarget{mp_ref_walter_94}{}
 A. Walter, D. Turner, J. Kim, M. Lyttle, P. M\"{u}ller, D. Mathews and M. Zuker (1994)\par
 Coaxial stacking of helices enhances binding of Oligoribonucleotides.., Proc. Natl. Acad. Sci. 91: 9218-\/9222
\item \label{mp_ref_shapiro_88}
\hypertarget{mp_ref_shapiro_88}{}
 B.A. Shapiro, (1988)\par
 An algorithm for comparing multiple RNA secondary structures, CABIOS 4, 381-\/393
\item \label{mp_ref_shapiro_90}
\hypertarget{mp_ref_shapiro_90}{}
 B.A. Shapiro and K. Zhang (1990)\par
 Comparing multiple RNA secondary structures using tree comparison, CABIOS 6, 309-\/318
\item \label{mp_ref_bruccoleri_88}
\hypertarget{mp_ref_bruccoleri_88}{}
 R. Bruccoleri and G. Heinrich (1988)\par
 An improved algorithm for nucleic acid secondary structure display, CABIOS 4, 167-\/173
\item \label{mp_ref_fontana_93a}
\hypertarget{mp_ref_fontana_93a}{}
 W. Fontana , D.A.M. Konings, P.F. Stadler, P. Schuster (1993) \par
 Statistics of RNA secondary structures, Biopolymers 33, 1389-\/1404
\item \label{mp_ref_fontana_93b}
\hypertarget{mp_ref_fontana_93b}{}
 W. Fontana, P.F. Stadler, E.G. Bornberg-\/Bauer, T. Griesmacher, I.L. Hofacker, M. Tacker, P. Tarazona, E.D. Weinberger, P. Schuster (1993)\par
 RNA folding and combinatory landscapes, Phys. Rev. E 47: 2083-\/2099
\item \label{mp_ref_hofacker_94a}
\hypertarget{mp_ref_hofacker_94a}{}
 I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994) Fast Folding and Comparison of RNA Secondary Structures. Monatshefte f. Chemie 125: 167-\/188
\item \label{mp_ref_hofacker_94b}
\hypertarget{mp_ref_hofacker_94b}{}
 I.L. Hofacker (1994) The Rules of the Evolutionary Game for RNA: A Statistical Characterization of the Sequence to Structure Mapping in RNA. PhD Thesis, University of Vienna.
\item \label{mp_ref_hofacker_02}
\hypertarget{mp_ref_hofacker_02}{}
 I.L. Hofacker, M. Fekete, P.F. Stadler (2002). Secondary Structure Prediction for Aligned RNA Sequences. J. Mol. Biol. 319:1059-\/1066
\item \label{mp_ref_adams_79}
\hypertarget{mp_ref_adams_79}{}
 D. Adams (1979)\par
 The hitchhiker's guide to the galaxy, Pan Books, London 
\end{DoxyEnumerate}