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) andVARNA
(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.
Developed by Das lab, Leland Stanford Junior University.
README by t47, April 2016. Updated, Rhiju Das, 2017.