C-version of SwiSpot

Download:
C-cmdline-SwiSpot-0.2.3.tar.gz.

Dependencies


Compiled version of ViennaRNA library must be linked at compile time. Tested with ViennaRNA 2.1.9 [It should work with newer versions]. Library path must be linked in CMakeLists.txt under the # Library Path section. ViennaRNA library header path must be given under the include_directory( ... )in CMakeLists.txt. ViennaRNA can be installed from Vienna TBI.

tar -zxvf ViennaRNA-2.1.9.tar.gz
cd ViennaRNA-2.1.9
./configure
make

optional

sudo make install

Mac OS X user can install ViennaRNA using homebrew:

brew install ViennaRNA


Installation

Unpack cmdline-SwiSpot-x.y.z.tar.gz

tar -zxvf cmdline-SwiSpot-x.y.z.tar.gz

Enter directory

cd cmdline-SwiSpot-x.y.z
mkdir build
cd build


Install:

cmake -G "Unix Makefiles" ../
make
make install

Installation notes

If you have any problem compiling ViennaRNA please refer to Vienna TBI. Moreover you could try linking against a never version of ViennaRNA.

Usage

 

Usage: SwiSpot -s sequence [-t temperature] [-o output] [-n number of structure ] [-pvlh]

SwiSpot is a command line utility for predicting riboswitch alternative
configurations. It is based upon the prediction of the so-called switching
sequence, to subsequently constrain the folding of the two functional structures.
While theoretically able to find any kind of switching behavior, uponnder the
assumption of sufficient representation in the ensemble of structures,
currently SwiSpot is able to classify only riboswitches that rely on
transcription termination via terminator hairpins, or translation inhibition
via SD sequestering/releasing.

OPTIONS:
  -s	   --sequence		  Sequence to be analyzed. Mandatory argument.

  -h	   --help		  Print help and exit

  -t	   --temperature	  Rescale energy parameters to a temperature of temp C. Default is 37C.

  -n	   --numstruct		  Number of structure used in the sampling procedure.

  -p	   --probability	  Use probability matrix instead of sampled ensemble.

  -o	   --output		  Write output to file.

  -c	   --confpath		  Configuration file path.

  -l	   --logging		  Turn verbosity on.

  -v	   --version		  Print version and exit.