Biers (Basic Inference Engine for RNA Structure)

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

• Secondary structure modeling from mutate-and-map (M2 and M2-seq) experiments.

• Secondary structure modeling guided by MOHCA data.

• Calculation of helix-wise confidence values using bootstrapping.

• Plotting utilities using MATLAB and VARNA.

Installation

To install Biers, simply:

• Download the zip or tar file of the repository and unpack; or

git clone https://github.com/ribokit/Biers.git

• In MATLAB, go to "Set Path". Then "Add with Subfolders" of the target path/to/Biers/Scripts/.

• Make sure you have set in your environment the variables DATAPATH (for RNAstructure) and VARNA (for VARNA). If you are on a Mac or Linux, put lines like the following in your .bashrc:

export DATAPATH=/path/to/RNAstructure/data_tables/
export VARNA=/path/to/src/VARNA.jar

Note that you should have set up DATAPATH as part of the RNAstructure installation process.

Usage

Documentation (MATLAB tutorial) is available at https://ribokit.github.io/Biers/.

License

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

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Developed by Das lab, Leland Stanford Junior University.

README by t47, April 2016. Updated, Rhiju Das, 2017.