Computational Tools: Difference between revisions

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<ul>
<ul>
<li>http://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software</li>
<li>http://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software</li>
<li>[https://getsatisfaction.com/eternagame/topics/quick_guide_to_vienna_rna_fold Quickguide to Vienna RNA fold]</li>
</ul>
</ul>
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<p>&nbsp;</p>
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</tbody>
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<p>&nbsp;</p>
<p>== Viewers ==</p>
<p>== Viewers ==</p>
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<p>Lab data analysis tool made by [[User:Omei|Omei]]. You can use this tool to group similar designs together, find good loops for  designing and for general design comparison. You can see the SHAPE numbers  while hovering over the SHAPE colors. For more about the tool, see Omei's [http://eternawiki.org/wiki/index.php5/User:Omei/Cloud_Lab_Data_Mining_Tool WIKI introduction].</p>
<p>Lab data analysis tool made by [[User:Omei|Omei]]. You can use this tool to group similar designs together, find good loops for  designing and for general design comparison. You can see the SHAPE numbers  while hovering over the SHAPE colors. For more about the tool, see Omei's [http://eternawiki.org/wiki/index.php5/User:Omei/Cloud_Lab_Data_Mining_Tool WIKI introduction].</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<h3>CSE tool - Computationally Selected Elements</h3>
<h3>LabDataMiner (LDM)</h3>
<p>Lab data search and analysis tool made by JandersonLee. This tool can be used to search for sequences and structures in our labs. This is a strong tool for digging out data across labs. Here is a link to the [http://166.78.137.98:8888/ldm.html tool]. For more about how to use the tool, it see the manual [http://eternawiki.org/wiki/index.php5/LabDataMiner here].</p>
<p>&nbsp;</p>
<h3>Computationally Selected Elements (CSE)</h3>
<p>Lab data analysis tool programmed by Jnicol. He based it on [https://getsatisfaction.com/eternagame/topics/computationally_selected_elements_analysis_tool_for_lab_data Mat's idea] for a lab  data  analysis tool. This tool will give you the average of the SHAPE score of whatever stretch of bases you put in and sort the data after the SHAPE score. This tool contains the early labs, but not the latests. Here is a link to the [http://www.amelior.com/cse5.php tool] and a [https://docs.google.com/document/d/1fMqiOoq681HrClp9Jcr-9q1K73a054xdzdoreGmQOhQ/edit manual].</p>
<p>Lab data analysis tool programmed by Jnicol. He based it on [https://getsatisfaction.com/eternagame/topics/computationally_selected_elements_analysis_tool_for_lab_data Mat's idea] for a lab  data  analysis tool. This tool will give you the average of the SHAPE score of whatever stretch of bases you put in and sort the data after the SHAPE score. This tool contains the early labs, but not the latests. Here is a link to the [http://www.amelior.com/cse5.php tool] and a [https://docs.google.com/document/d/1fMqiOoq681HrClp9Jcr-9q1K73a054xdzdoreGmQOhQ/edit manual].</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p>[[/EteRNA scripts|EteRNA scripts]]</p>
<p>[[/EteRNA scripts|EteRNA scripts]]</p>

Revision as of 00:32, 13 December 2013

 

 

== Folding (Structure prediction) ==

<tbody> </tbody>
Name Online server Sources and/or binaries
ViennaRNA http://rna.tbi.univie.ac.at/ http://www.tbi.univie.ac.at/~ronny/RNA/index.html

 

=== See also ===

 

== Design (Inverse Folding) ==

<tbody> </tbody>
Name Server Sources and/or binaries
NUPACK http://nupack.org/ http://nupack.org/downloads

 

 

== Viewers ==

=== 2D viewers ===

<tbody> </tbody>
Name Server Sources and/or binaries
VARNA http://varna.lri.fr/  

 

=== 3D viewers ===

<tbody> </tbody>
Name Server Sources and/or binaries
UCSF Chimera http://www.cgl.ucsf.edu/chimera/  http://www.cgl.ucsf.edu/chimera/download.html

 

== Lab results analysis ==

=== Data mining ===

Here are two data mining tools that are open source and have lots of built in functionality: FAKE with GAME, or its replacement Rapid-I (it's huge). All types of modeling supported. GUI drag & drop model building.

http://sourceforge.net/projects/fakegame/

http://rapid-i.com/

 

Player created tools

 

Cloud Lab Data Mining Tool

Lab data analysis tool made by Omei. You can use this tool to group similar designs together, find good loops for designing and for general design comparison. You can see the SHAPE numbers while hovering over the SHAPE colors. For more about the tool, see Omei's WIKI introduction.

 

LabDataMiner (LDM)

Lab data search and analysis tool made by JandersonLee. This tool can be used to search for sequences and structures in our labs. This is a strong tool for digging out data across labs. Here is a link to the tool. For more about how to use the tool, it see the manual here.

 

Computationally Selected Elements (CSE)

Lab data analysis tool programmed by Jnicol. He based it on Mat's idea for a lab data analysis tool. This tool will give you the average of the SHAPE score of whatever stretch of bases you put in and sort the data after the SHAPE score. This tool contains the early labs, but not the latests. Here is a link to the tool and a manual.

 

EteRNA scripts