Choose Your Workflow
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I have just discovered an RNA molecule
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I want to learn an RNA’s secondary structure
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I want to test an RNA secondary structure model
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I think my RNA has interesting alternative states
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I think my RNA has a 3D structure
About
RiboKit brings together RNA modeling & analysis packages that have been developed and are maintained by the Das Lab and collaborators since 2009. The focus is on multidimensional chemical mapping methods for RNA structure inference. This site is maintained at the Department of Biochemistry, Stanford University School of Medicine. Being an academic effort, it’s not perfect. If you need help, or have suggestions that will help your research, please send an e-mail to ribokit.info [at] gmail.com.
Packages in RiboKit
| Package | Description | Language |
|---|---|---|
| Biers | Secondary structure analysis from chemical mapping | MATLAB |
| HiTRACE | Quantitation of capillary electrophoresis MCM data | MATLAB |
| LIFFT | Thermodynamic parameters from chemical mapping | MATLAB |
| M2seq | Quantitation of Illumina-based mutate-and-map data | C++/MATLAB |
| MAPseeker | Quantitation of Illumina-based MAP/MOHCA data | C++/MATLAB |
| Primerize | Easy assembly of templates for RNA synthesis | Python |
| RDATKit | Utilities for RDAT data format | Python & MATLAB |
| REEFFIT | Analysis of multi-state RNAs from mutate-and-map data | Python |
| RiboPaint | Publication-quality secondary structure diagram painter | MATLAB |
| RiboVis | Easy-to-install PyMOL utilities for RNA visualization | Python |
Experimental protocols that go with the tools above are compiled on the Protocols page.