This repository contains scripts and libraries to design transcriptional riboswitches and optimize them for a specific sequence context.

If you use this software for your research, please cite:

C Günzel, F Kühnl, K Arnold, S Findeiß, C Weinberg, PF Stadler, and Mario Mörl, "Beyond Plug and Pray: Context Sensitivity and in silico Design of Artificial Neomycin Riboswitches", submitted

Copyright 2015-2020 Sven Findeiß & Felix Kühnl

The code provided in this package is free software released under the GNU General Public License v3. Please refer to file LICENSE.

The README.md files in each of the subdirectories contain per-task instructions to install dependencies and perform the desired step.

Generally, we recommend the usage of the package manager Conda / Bioconda to provide all required dependencies. To install Conda, run the following commands:

curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh

You may need to restart your shell. Next, set up the Bioconda channels:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Finally, update Conda to the latest version:

conda update --yes conda

Now, please follow the instructions in the README.md files in the subdirectories for the task you want to perform.

Futher information can be found in the official Bioconda docs: https://bioconda.github.io/user/install.html