REEFFIT (RNA Ensemble Extraction From Footprinting Insights Technique)

REEFFIT is a method to fit RNA secondary structure ensembles to multi-dimensional chemical mapping data. Currently, the method can take data from one and multiple mutate-and-map or mutate-bind-and-map (mutate-and-map plus ligand titrations, e.g. for riboswitches) experiments. Output is a set of weights and expected reactivities for each structure that linearly combine to form the data. If the structural ensemble is not provided, REEFFIT uses RNAstructure to generate a suboptimal set of structures of all mutants.

Installation

To install REEFFIT, simply:

• Run:

cd path/to/REEFFIT/repo
python setup.py install

For system-wide installation, you must have permissions and use with sudo.

REEFFIT requires the following Python packages as dependencies, all of which can be installed through pip.

cvxopt >= 1.1.6
joblib >= 0.5.4
matplotlib >= 1.1.1
numpy >= 1.6.1
scipy >= 0.9.0
pymc >= 2.2

rdatkit >= 1.0.4

• Note that you should have RDATKit installed and properly set up as well (see https://github.com/ribokit/RDATKit)

• In your profile (e.g. ~/.bashrc), include an environment variable REEFFIT_HOME that points to the REEFFIT home directory, e.g.:

export REEFFIT_HOME=path/to/REEFFIT/repo

• Be sure to add REEFFIT_HOME/bin to your PATH. Similarly in ~/.bashrc or ~/.bash_profile, include:

export PATH=$PATH:$REEFFIT_HOME/bin

• Check that REEFFIT is correctly installed. Test the reeffit command by running reeffit -h in your shell.

Documentation

Documentation is available at https://reeffit.readthedocs.org/ or https://ribokit.github.io/REEFFIT/.

License

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

Reference

Cordero, P., and Das, R. (2015)
Rich structure landscapes in both natural and artificial RNAs revealed by mutate-and-map analysis.
PLOS Computational Biology 11 (11): e1004473.

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Developed by Das lab, Leland Stanford Junior University.

README by t47, May 2016.