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[jabaws.git] / binaries / src / ViennaRNA / doc / latex / group__cofold.tex

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+\hypertarget{group__cofold}{\section{Calculate Secondary Structures of two R\-N\-As upon Dimerization}
+\label{group__cofold}\index{Calculate Secondary Structures of two R\-N\-As upon Dimerization@{Calculate Secondary Structures of two R\-N\-As upon Dimerization}}
+}
+
+
+Predict structures formed by two molecules upon hybridization.  
+
+
+Collaboration diagram for Calculate Secondary Structures of two R\-N\-As upon Dimerization\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=350pt]{group__cofold}
+\end{center}
+\end{figure}
+\subsection*{Modules}
+\begin{DoxyCompactItemize}
+\item 
+\hyperlink{group__mfe__cofold}{M\-F\-E Structures of two hybridized Sequences}
+\item 
+\hyperlink{group__pf__cofold}{Partition Function for two hybridized Sequences}
+\begin{DoxyCompactList}\small\item\em Partition Function Cofolding. \end{DoxyCompactList}\item 
+\hyperlink{group__up__cofold}{Partition Function for two hybridized Sequences as a stepwise Process}
+\begin{DoxyCompactList}\small\item\em Partition Function Cofolding as a stepwise process. \end{DoxyCompactList}\end{DoxyCompactItemize}
+
+
+\subsection{Detailed Description}
+Predict structures formed by two molecules upon hybridization. The function of an R\-N\-A molecule often depends on its interaction with other R\-N\-As. The following routines therefore allow to predict structures formed by two R\-N\-A molecules upon hybridization.\par
+ One approach to co-\/folding two R\-N\-As consists of concatenating the two sequences and keeping track of the concatenation point in all energy evaluations. Correspondingly, many of the \hyperlink{group__mfe__cofold_gabc8517f22cfe70595ee81fc837910d52}{cofold()} and \hyperlink{group__pf__cofold_gaa86a5f998789ed71813d23d7307a791b}{co\-\_\-pf\-\_\-fold()} routines below take one sequence string as argument and use the the global variable \hyperlink{fold__vars_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{cut\-\_\-point} to mark the concatenation point. Note that while the {\itshape R\-N\-Acofold} program uses the '\&' character to mark the chain break in its input, you should not use an '\&' when using the library routines (set \hyperlink{fold__vars_8h_ab9b2c3a37a5516614c06d0ab54b97cda}{cut\-\_\-point} instead).\par
+ In a second approach to co-\/folding two R\-N\-As, cofolding is seen as a stepwise process. In the first step the probability of an unpaired region is calculated and in a second step this probability of an unpaired region is multiplied with the probability of an interaction between the two R\-N\-As. This approach is implemented for the interaction between a long target sequence and a short ligand R\-N\-A. Function \hyperlink{group__up__cofold_ga5b4ee40e190d2f633cd01cf0d2fe93cf}{pf\-\_\-unstru()} calculates the partition function over all unpaired regions in the input sequence. Function \hyperlink{group__up__cofold_ga1aa0aa02bc3a724f87360c03097afd00}{pf\-\_\-interact()}, which calculates the partition function over all possible interactions between two sequences, needs both sequence as separate strings as input. 
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