Answers.Body: <p>The RNA viewer that is particularly good is <a href="http://varna.lri.fr" rel="nofollow noreferrer">VA RNA</a>. This stands for &quot;Visualisation Applet for RNA&quot;. Its a java app and run it via,</p>
  <pre><code>java -jar /Route2Progam/vaRNA/VARNAv3-93-API.jar
  </code></pre>
  <p>Where <code>Route2Progam</code> is the path to where the jar files is stored, all other info in the run code is literal.</p>
  <p>Very nice pictures, point and clicky, drag structures into different shapes and easy to colour ... so for a GUI its great.</p>
  <p>They recommend <a href="http://wilab.inha.ac.kr/pseudoviewer/" rel="nofollow noreferrer">PsuedoViewer</a> for psuedoknots, but if that doesn't mean much ... it doesn't matter.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-01-22T23:58:26.600Z
Answers.LastActivityDate: 2023-01-23T04:14:53.973Z
Answers.LastEditDate: 2023-01-23T04:14:53.973Z
Answers.UserDisplayName: M__
Answers.Body: <p>You could try mxfold2.
  <a href="https://github.com/mxfold/mxfold2" rel="nofollow noreferrer">https://github.com/mxfold/mxfold2</a></p>
  <pre><code>% mxfold2 predict test.fa
  &gt;DS4440
  GGAUGGAUGUCUGAGCGGUUGAAAGAGUCGGUCUUGAAAACCGAAGUAUUGAUAGGAAUACCGGGGGUUCGAAUCCCUCUCCAUCCG
  (((((((........(((((..((((.....))))...)))))...................(((((.......)))))))))))). (24.8)
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
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Answers.LastActivityDate: 2023-01-23T03:33:00.400Z
Answers.UserDisplayName: Supertech
Body: <p>I want to manually fold and pair two sequences (U4 and U6). And I want to make niceish figures.</p>
  <p>I haven't found a single program that does that.</p>
  <p>thanks</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-01-22T23:37:49.610Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-01-22T23:42:08.640Z
Comments.Text: Hi @user3392394 and welcome. The question is difficult to understand. Are you trying to perform two individual RNA structures, or is this two sequences to make a single structure? There are lots of programs for RNA structure, what I suspect is you have a specific project in mind, which is not being clearly communicated. Alternatively are you just looking for a RNA 2D structure viewer?
Comments.UserDisplayName: M__
Tags: <visualization><rna>
Title: Is there a tool to visualize RNA secondary structure?
ThreadText: # Is there a tool to visualize RNA secondary structure?
  
  (Asked by: username_0 on 2023-01-22)
  
  I want to manually fold and pair two sequences (U4 and U6). And I want to make niceish figures.
  
  I haven't found a single program that does that.
  
  thanks
  
  **Tags:** visualization, rna
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_2**: Hi @username_0 and welcome. The question is difficult to understand. Are you trying to perform two individual RNA structures, or is this two sequences to make a single structure? There are lots of programs for RNA structure, what I suspect is you have a specific project in mind, which is not being clearly communicated. Alternatively are you just looking for a RNA 2D structure viewer?  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2023-01-22. Score: 1
  
  The RNA viewer that is particularly good is [VA RNA](http://varna.lri.fr). This stands for "Visualisation Applet for RNA". Its a java app and run it via,
  
  ```
  java -jar /Route2Progam/vaRNA/VARNAv3-93-API.jar
  
  ```
  
  Where `Route2Progam` is the path to where the jar files is stored, all other info in the run code is literal.
  
  Very nice pictures, point and clicky, drag structures into different shapes and easy to colour ... so for a GUI its great.
  
  They recommend [PsuedoViewer](http://wilab.inha.ac.kr/pseudoviewer/) for psuedoknots, but if that doesn't mean much ... it doesn't matter.
  
  
  ---
  
  ### Answer by username_3 on 2023-01-23. Score: 1
  
  You could try mxfold2.
  <https://github.com/mxfold/mxfold2>
  
  ```
  % mxfold2 predict test.fa
  >DS4440
  GGAUGGAUGUCUGAGCGGUUGAAAGAGUCGGUCUUGAAAACCGAAGUAUUGAUAGGAAUACCGGGGGUUCGAAUCCCUCUCCAUCCG
  (((((((........(((((..((((.....))))...)))))...................(((((.......)))))))))))). (24.8)
  
  ```
  
  
  ---
  
  