DrConverters: unified cotranscriptional folding output.

This repository contains scripts to convert the output of different cotranscriptional folding simulators into the *.drf file format. This format is used for visualization by the JavaScript application DrForna. Note that the DrTransformer package for cotranscriptional folding natively supports the drf file format, and so this format can also be plotted in various flavors by the Python script DrPlotter from the DrTransformer package.

Installation

The scripts provided in this repository can be installed using:

pip install .

Note: This repository only provides functions to convert output from other programs, as well as wrapper scripts to call those programs and convert output automatically. The respective dependencies must be installed separately (see below).

Dependencies

Kinfold [Flamm et al. (2000)] & ViennaRNA [Lorenz et al. (2011)]

Kinfold is part of the ViennaRNA package, which can be installed via bioconda. First, make sure bioconda is set up properly with:

  ~$ conda config --add channels defaults
  ~$ conda config --add channels bioconda
  ~$ conda config --add channels conda-forge
  ~$ conda config --set channel_priority strict

Second, install or update your ViennaRNA installation.

  ~$ conda install 'viennarna>=2.5.1'

Kinefold [Xayaphoummine et al. (2005)]

Kinefold must be downloaded (follow the link Kinefold). It is important to have the executable kinefold_long_static placed in the working directory where DrKinefold is used. DrKinefold also depends on ViennaRNA (>=2.5.1), due to library functions that help with the conversion of Kinefold output to pseudoknotted dot-bracket strings.

Testing

Test the functionality of wrapper scripts via:

DrKinfold --help
DrKinefold --help

Contributing

Did you find a bug? Or do you want to provide support for a different cotranscriptional folding software? Please fork the repository and submit a pull request.

Cites

The program wrappers provided in this repository use published software. Use them at your own risk -- ask if you have questions -- and do not forget to cite the original software:

• DrKinfold depends on Kinfold, publised in Flamm et al. (2000)
• DrKinefold depends on Kinefold, published in Xayaphoummine et al. (2005)

The *.drf output format was primarily developed for DrForna visualization. If you find this visualization helpful during your analysis, consider citing Tanasie et al. (2023).

The program DrPlotter provides additional Python visualization options, it is part of the DrTransformer Python package, which should be cited as Badelt et al. (2023).