Computational Tools

 

 

== 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 ===

• http://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software

 

== 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.

 

CSE tool - Computationally Selected Elements

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.