Contains three software implementations of CCJ.
CCJ is a MFE (minimum free energy) based method for predicting the psuedoknotted secondary structures of RNA sequences.
There are three different versions of CCJ that are compared for the WABI 2017 paper submission.
For general usage, Sparse CCJ is recommended to be used.
CCJ should work on most Linux or Mac machines.
The different versions are as follows:
Original CCJ is the original CCJ detailed in "Algorithms for prediction of RNA pseudoknotted secondary structures".
Modified CCJ is a version of Original CCJ that uses the DP09 energy model.
Sparse CCJ is a "sparsified" version of Modified CCJ that uses less memory than any of the other versions.
SimFold is contained in the Simfold subdirectory and is required to be installed as a library before using any version of CCJ.
Original CCJ is contained in the Original_CCJ subdirectory.
Sparse CCJ is contained in the Sparse_CCJ subdirectory.
Modified CCJ is used by running Sparse CCJ with a special argument. This is detailed in the README.md in the Sparse_CCJ subdirectory.
Instructions for usage are in the READMEs of the respective subdirectories.
Requirements: A compiler that supports C++11 standard (tested with g++ version 4.7.2 or higher) and CMake version 3.1 or greater.
CMake version 3.1 or greater must be installed in a way that CCJ can find it.
To test if your Mac or Linux system already has CMake, you can type into a terminal:
cmake --version
If it does not print a cmake version greater than or equal to 3.1, you will have to install CMake depending on your operating system.
Easiest way is to install homebrew and use that to install CMake.
To do so, run the following from a terminal to install homebrew:
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
When that finishes, run the following from a terminal to install CMake.
brew install cmake
Run from a terminal
wget http://www.cmake.org/files/v3.8/cmake-3.8.2.tar.gz
tar xzf cmake-3.8.2.tar.gz
cd cmake-3.8.2
./configure
make
make install
- Download the repository and extract the files onto your system.
- From a command line in the root directory (where this README.md is) run
cmake -H. -Bbuild
cmake --build build
If you are getting errors about your comiler not having C++11 features, you may need to specify a specific compiler, such as g++. If you want to do so you can instead run something like
cmake -H. -Bbuild -DCMAKE_CXX_COMPILER=g++
cmake --build build
- Run CCJ by navigating to the directory of the CCJ version you wish to use and following the usage instructions in the README.md of that directory.
Sparse_CCJ Readme (recommended)
Original_CCJ Readme
After installing you can move the executables wherever you wish, but you should not delete or move the simfold folder, or you must recompile the executables. If you move the folders and wish to recompile, you should first delete the created "build" folder before recompiling.
SimFold is a part of MultiRNAFold (http://www.rnasoft.ca/download.html).
CCJ and MultiRNAFold are copyrighted under GNU General Public Licence.
Although the authors have made every effort to ensure that CCJ correctly implements the underlying models and fullfills the functions described in the documentation, neither the authors nor the University of Alberta guarantee its correctness, fitness for a particular purpose, or future availability.
If you have any issues or feature requests, please contact Hosna Jabbari: jabbari at ualberta dot ca.