Computational Tools

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Contents

 

Folding (Structure prediction)

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)

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

 

 

Viewers

2D viewers

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

 

3D viewers

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

Personal tools
Main page
Introduction to the Game