FFTbor

FFTbor computes number of delta-neighbours and the partition function of delta-neighbours.

Type FFTbor --help for help on the input format.

Dependencies

This software depends on the presence of the following programs:

1. A valid C++ compiler with OpenMP support (developed using GCC 4.8 but should support any reasonable C++98 compiler)
2. CMake (>= 2.6, to generate the Makefile)
3. FFTW (= 3.3.x)
4. libRNA.a from the ViennaRNA package (= 2.x)

Installation

To compile the program using CMake, perform the following commands:

cd build
cmake -DCMAKE_INSTALL_PREFIX=/usr/local ..
make
make install

Installation Notes:

• If libRNA.a is in a non-standard location, you can specify its path with the -CMAKE_LIBRARY_PATH flag.
  • See this list of CMake environment flags for more details.
• The -DCMAKE_INSTALL_PREFIX flag is not strictly necessary, and uses /usr/local as a default.
• make install may need administrator privileges, depending on the permissions of your target install prefix.
• CMake >= 2.6 is required to generate the system-appropriate Makefile.

Relevant Files

• main.c - the main program file, reads input and prints output.
• delta.c, delta.h - the algorithm implementation.
• misc.c, misc.h - a few additional functions and global variables.
• energy_const.h, energy_par.h, params.h - three h-files from ViennaRNA, these define energy parameters.
• rna_turner1999.par, rna_turner2004.par - the energy parameters (in the Vienna 2.x format).
• libRNA.a - Vienna RNA library file, this file is not included in this tar-ball, but is generated by compiling the Vienna RNA package.
• CMakeLists.txt - the CMake manifest for this package.