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README.md

silentMutations

This tool can automatically construct interrupting and restoring silent mutation pairs within coding regions for combinatorial in-silico analysis of RNA-RNA interactions. The tool has been written in Python 3.6.5 and relies heavily on the RNAcofold python site-package of the ViennaRNA Package 2.4.

Mandatory Prerequisites

Conda Installation

Installing everything with Conda:

conda install -c bioconda  viennarna=2.4.13
conda install -c conda-forge numpy=1.16.4
conda install -c lb_arrakistx varna=3.93
git clone https://github.com/desiro/silentMutations.git 

Docker Installation

Using Docker Hub:

docker run --user $(id -u):$(id -g) --rm -v <your working directory>:/source --workdir /source desiro/sim silentMutations.py -p example -f example.fa -s1 seq1:2:20-36 -s2 seq2:0:23-44 -cls ssRNA- -r -c -thr=4
  • It is currently not possible to use VARNA within the Docker Hub repository due to some java issues.

Unix Installation

Installing the ViennaRNA package on Linux:

tar -zxvf ViennaRNA-2.4.9.tar.gz
cd ViennaRNA-2.4.9
./configure --with-python3
make
sudo make install

Installing the ViennaRNA package on MAC:

tar -zxvf ViennaRNA-2.4.9.tar.gz
cd ViennaRNA-2.4.9
./configure --enable-universal-binary --with-python3
make
sudo make install

For Windows 10 users, please use the Ubuntu subsystem and follow the Linux installation steps.

Optional Prerequisites

Examples

The basic input for silentMutations.py includes the following parameters:

  • -p - name of the output folder
  • -f - input fasta file, will only read the first two sequences
  • -s1 <name>:<frame>:<start>-<end> - for the first sequence
  • -s2 <name>:<frame>:<start>-<end> - for the second sequence

Basic Example

python3 silentMutations.py -p example -f example.fa -s1 seq1:2:20-36 -s2 seq2:0:23-44 -cls ssRNA- -r -c -thr=4

Example with VARNA and Inkscape

python3 silentMutations.py -p example -f example.fa -s1 seq1:2:20-36 -s2 seq2:0:23-44 -cls ssRNA- -r -c -thr=4 -var VARNAv3-93.jar -ink inkscape

Authors

License

This project is licensed under the GNU General Public License v3.0 - see the LICENSE file for details.

Reference

Please cite SilentMutations if you find our tool useful. There is also an open access version at bioRxiv.

Workflow overview

workflow

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