Computational Tools: Difference between revisions
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<p> </p> | |||
<p>__TOC__</p> | |||
<p> </p> | |||
<p>== Folding (Structure prediction) ==</p> | |||
<table border="0" cellpadding="3"> | |||
<tbody> | |||
<tr> | |||
<td>Name</td> | |||
<td>Online server</td> | |||
<td>Sources and/or binaries</td> | |||
</tr> | |||
<tr> | |||
<td>ViennaRNA</td> | |||
<td>http://rna.tbi.univie.ac.at/</td> | |||
<td>http://www.tbi.univie.ac.at/~ronny/RNA/index.html</td> | |||
</tr> | |||
</tbody> | |||
</table> | |||
<p> </p> | |||
<p>=== See also ===</p> | |||
<ul> | |||
<li>http://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software</li> | |||
</ul> | |||
<p> </p> | |||
<p>== Design (Inverse Folding) ==</p> | |||
<table border="0" cellpadding="3"> | |||
<tbody> | |||
<tr> | |||
<td>Name</td> | |||
<td>Server</td> | |||
<td>Sources and/or binaries</td> | |||
</tr> | |||
<tr> | |||
<td>NUPACK</td> | |||
<td>http://nupack.org/</td> | |||
<td>http://nupack.org/downloads</td> | |||
</tr> | |||
</tbody> | |||
</table> | |||
<p> </p> | |||
<p>== Viewers ==</p> | |||
<p>=== 2D viewers ===</p> | |||
<table border="0" cellpadding="3"> | |||
<tbody> | |||
<tr> | |||
<td>Name</td> | |||
<td>Server</td> | |||
<td>Sources and/or binaries</td> | |||
</tr> | |||
<tr> | |||
<td>VARNA</td> | |||
<td>http://varna.lri.fr/</td> | |||
<td> </td> | |||
</tr> | |||
</tbody> | |||
</table> | |||
<p> </p> | |||
<p>=== 3D viewers ===</p> | |||
<table border="0" cellpadding="3"> | |||
<tbody> | |||
<tr> | |||
<td>Name</td> | |||
<td>Server</td> | |||
<td>Sources and/or binaries</td> | |||
</tr> | |||
<tr> | |||
<td>UCSF Chimera</td> | |||
<td>http://www.cgl.ucsf.edu/chimera/</td> | |||
<td> http://www.cgl.ucsf.edu/chimera/download.html</td> | |||
</tr> | |||
</tbody> | |||
</table> | |||
<p> </p> | |||
<p>== Lab results analysis ==</p> | |||
<p>=== Data mining ===</p> | |||
<p>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.</p> | <p>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.</p> | ||
<p>http://sourceforge.net/projects/fakegame/</p> | <p>http://sourceforge.net/projects/fakegame/</p> | ||
<p>http://rapid-i.com/</p> | <p>http://rapid-i.com/</p> | ||
Revision as of 14:27, 10 October 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.
