Biers

Biers is a set of MATLAB scripts that wrap around the RNAstructure suite of executables to infer secondary structure models guided by chemical mapping data. Features include:

• Secondary structure modeling guided by SHAPE and DMS probing, as well as data from mutate-and-map experiments.
• Secondary structure modeling guided by MOHCA data.
• Calculation of helix-wise confidence values using bootstrapping.
• Plotting utilities using MATLAB and VARNA.

Installation

• Biers MATLAB instructions

• Dependency

Usage

MATLAB Tutorial is available for:

• Predict Secondary Structure
• Visualize Secondary Structure

License

Copyright © of Biers Source Code is described in LICENSE.md.

Reference

Tian, S., Cordero, P., Kladwang, W., and Das, R. (2014)
High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states
RNA 20 (11): 1815 - 1826. | Paper | Link

Kladwang, W., VanLang, C.C., Cordero P., and Das, R. (2011)
A two-dimensional mutate-and-map strategy for non-coding RNA structure
Nature Chemistry 3: 954 - 962. | Paper | Link

Related Packages

• HiTRACE
• MAPSeeker
• RDATKit

Workflows

• I have just discovered an RNA molecule
• I want to learn an RNA’s secondary structure
• I think my RNA has interesting alternative states

Developed by Das lab, Leland Stanford Junior University.

README by t47, April 2016.

• Next: MATLAB installation