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+<h1>Calculate Secondary Structures of two RNAs upon Dimerization<br/>
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+[<a class="el" href="group__folding__routines.html">RNA Secondary Structure Folding</a>]</small>
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<p>Predict structures formed by two molecules upon hybridization.
-<a href="#details">More...</a></p>
-<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
- <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Collaboration diagram for Calculate Secondary Structures of two RNAs upon Dimerization:</div>
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+Collaboration diagram for Calculate Secondary Structures of two RNAs upon Dimerization:</div>
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-<tr class="memitem:group__mfe__cofold"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__cofold.html">MFE Structures of two hybridized Sequences</a></td></tr>
-<tr class="memitem:group__pf__cofold"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html">Partition Function for two hybridized Sequences</a></td></tr>
-<tr class="memdesc:group__pf__cofold"><td class="mdescLeft"> </td><td class="mdescRight">Partition Function Cofolding. <br/></td></tr>
-<tr class="memitem:group__up__cofold"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__up__cofold.html">Partition Function for two hybridized Sequences as a stepwise Process</a></td></tr>
-<tr class="memdesc:group__up__cofold"><td class="mdescLeft"> </td><td class="mdescRight">Partition Function Cofolding as a stepwise process. <br/></td></tr>
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+<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__mfe__cofold.html">MFE Structures of two hybridized Sequences</a></td></tr>
+<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__pf__cofold.html">Partition Function for two hybridized Sequences</a></td></tr>
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+<p><tr><td class="mdescLeft"> </td><td class="mdescRight"><p>Partition Function Cofolding. </p>
+<br/></td></tr>
+</p>
+<tr><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="group__up__cofold.html">Partition Function for two hybridized Sequences as a stepwise Process</a></td></tr>
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+<p><tr><td class="mdescLeft"> </td><td class="mdescRight"><p>Partition Function Cofolding as a stepwise process. </p>
+<br/></td></tr>
+</p>
</table>
-<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
+<hr/><a name="_details"></a><h2>Detailed Description</h2>
<p>Predict structures formed by two molecules upon hybridization. </p>
<p>The function of an RNA molecule often depends on its interaction with other RNAs. The following routines therefore allow to predict structures formed by two RNA molecules upon hybridization.<br/>
- One approach to co-folding two RNAs consists of concatenating the two sequences and keeping track of the concatenation point in all energy evaluations. Correspondingly, many of the <a class="el" href="group__mfe__cofold.html#gabc8517f22cfe70595ee81fc837910d52" title="Compute the minimum free energy of two interacting RNA molecules.">cofold()</a> and <a class="el" href="group__pf__cofold.html#gaa86a5f998789ed71813d23d7307a791b" title="Calculate partition function and base pair probabilities.">co_pf_fold()</a> routines below take one sequence string as argument and use the the global variable <a class="el" href="fold__vars_8h.html#ab9b2c3a37a5516614c06d0ab54b97cda" title="Marks the position (starting from 1) of the first nucleotide of the second molecule within the concat...">cut_point</a> to mark the concatenation point. Note that while the <em>RNAcofold</em> program uses the '&' character to mark the chain break in its input, you should not use an '&' when using the library routines (set <a class="el" href="fold__vars_8h.html#ab9b2c3a37a5516614c06d0ab54b97cda" title="Marks the position (starting from 1) of the first nucleotide of the second molecule within the concat...">cut_point</a> instead).<br/>
+ One approach to co-folding two RNAs consists of concatenating the two sequences and keeping track of the concatenation point in all energy evaluations. Correspondingly, many of the <a class="el" href="group__mfe__cofold.html#gabc8517f22cfe70595ee81fc837910d52" title="Compute the minimum free energy of two interacting RNA molecules.">cofold()</a> and <a class="el" href="group__pf__cofold.html#gaa86a5f998789ed71813d23d7307a791b" title="Calculate partition function and base pair probabilities.">co_pf_fold()</a> routines below take one sequence string as argument and use the the global variable <a class="el" href="fold__vars_8h.html#ab9b2c3a37a5516614c06d0ab54b97cda" title="Marks the position (starting from 1) of the first nucleotide of the second molecule...">cut_point</a> to mark the concatenation point. Note that while the <em>RNAcofold</em> program uses the '&' character to mark the chain break in its input, you should not use an '&' when using the library routines (set <a class="el" href="fold__vars_8h.html#ab9b2c3a37a5516614c06d0ab54b97cda" title="Marks the position (starting from 1) of the first nucleotide of the second molecule...">cut_point</a> instead).<br/>
In a second approach to co-folding two RNAs, 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 RNAs. This approach is implemented for the interaction between a long target sequence and a short ligand RNA. Function <a class="el" href="group__up__cofold.html#ga5b4ee40e190d2f633cd01cf0d2fe93cf" title="Calculate the partition function over all unpaired regions of a maximal length.">pf_unstru()</a> calculates the partition function over all unpaired regions in the input sequence. Function <a class="el" href="group__up__cofold.html#ga1aa0aa02bc3a724f87360c03097afd00" title="Calculates the probability of a local interaction between two sequences.">pf_interact()</a>, which calculates the partition function over all possible interactions between two sequences, needs both sequence as separate strings as input. </p>
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