Tools for High-throughput RNA Structure Analysis

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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.

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