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 ===
== 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/
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 [1] tool and a manual.