RNAMake
RNAMake is a toolkit for designing and optimizing RNA 3D structure. It allows the alignment between RNA motifs. These motif are small modular peices of RNA that are believed to fold independently, thus attaching them together with helix flanking both sides allows users of RNAMake to build large segments of RNA with a high success rate of forming the predicted structure in vitro.
Dependencies
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Python Dependencies: The required dependencies to build the software are Python >= 2.7, Numpy >= 1.6, Matplotlib >= 1.1.0, simplejson >= 3.8.
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C++ Dependencies: Either g++ or clang installed on system and also Ninja (https://ninja-build.org/) and CMake (https://cmake.org/)
Installation
Python Module
To install RNAMake, simply:
- From GitHub, download the zip or tar file of the repository and unpack; or
git clone https://github.com/jyesselm/RNAMake.git
To make sure you system can find the RNAMake folder into the system’s $PATH and $PYTHONPATH. In bash this can be done by adding the following lines to your ~/.bashrc or ~/.bash_profile if you are using a mac:
export RNAMAKE=<RNAMake Path>
export PATH=$PATH:<RNAMake Path>
export PYTHONPATH=$PYTHONPATH:<RNAMake Path>
Afterwards make sure to source your bashrc file.
source ~/.bashrc
To make sure everything is working run the first example module
python <RNAMake Path>/examples/example_motif.py
Compiling C++ Programs (Optional)
An additional optional step is to compile the c++ verision of RNAMake. All the functionality is redundant but it is significantly faster. Performing large design jobs, its recommended to use the C++ programs instead of python.
cd <RNAMake Path>/rnamake/lib/RNAMake/cmake/build
python make_project.py
cmake -G Ninja
ninja
To test run:
python run_unittests.py
This will run all the unittests for the c++ code. This may take a few minutes but will ensure everything is working properly.
Documentation
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Python Documentation is available at: http://jyesselm.github.io/RNAMake/.
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C++ Documentation is available at: http://jyesselm.github.io/RNAMake/html_cpp/index.html.
License
Copyright © of RNAMake Source Code is described in LICENSE.md.
Related Packages
Workflows
Developed by Das lab, Leland Stanford Junior University.