mdondrup / rnafinder

RNAfinder

RNafinder is used to search for and identify RNAs. It is a wrapper around a search tool called erpin

This package is based on activities of the OGMP (i.e, priori to 2002), and becomes open source as part of MFannot.

Install

In order to run RNAfinder you need:

1. Install erpin on your system.

wget http://rssf.i2bc.paris-saclay.fr/download/Erpin/erpin5.5.4.serv.tar.gz    
tar -xvzf erpin5.5.4.serv.tar.gz    
cd erpin5.5.4.serv
make
# Add erpin (`bin/erpin`) to $PATH
cp bin/erpin ~/bin/.

2. Install the PirObject library.

git clone https://github.com/prioux/PirObject
# Add `PirObject.pm` to @INC (Perl package path)
sudo cp PirObject/lib/PirObject.pm /usr/share/perl5/.

3. Install all the necessary PirModels.

sudo git clone https://github.com/BFL-lab/PirModels ~/PirModels

4. Install the BioPerl library Bio::Tools::CodonTable

sudo cpanm Bio::Tools::CodonTable

5. Copy the DOT_RNAfinder.cfg in your home directory under .RNAfinder.cfg or under the directory defined by the RNAFINDER_CFG_PATH environment variable.

cp DOT_RNAfinder.cfg .RNAfinder.cfg
echo "export RNAFINDER_CFG_PATH=`pwd`" >> ~/.bashrc
source ~/.bashrc

6. Copy RNAfinder file in one of your executable directory (e.g: a directory list in $PATH).

cp RNAfinder ~/bin/.

7. Add the models needed for the run

git clone https://github.com/BFL-lab/MFannot_data
echo "# MFannot data installation" >>mfannot-data
echo "export EGC=`pwd`/MFannot_data/EGC" >>mfannot-data
echo "export MFANNOT_EXT_CFG_PATH=`pwd`/MFannot_data/config" >>mfannot-data
echo "export MFANNOT_MOD_PATH=`pwd`/MFannot_data/models" >>mfannot-data
echo "export ERPIN_MOD_PATH=`pwd`/MFannot_data/models/Erpin_models" >>mfannot-data
echo "export MFANNOT_LIB_PATH=`pwd`/MFannot_data/protein_collections" >>mfannot-data
cat mfannot-data >>~/.bashrc
source ~/.bashrc

Note: At this point the installation of RNAfinder was only tested on Unix systems (Ubuntu and CentOS).

Usage

In order to get the help page of RNAfinder you need to type RNAfinder -h in your terminal.

Models

• rns
• tRNA
• rnpB
• rrn5
• IntronI
• IntronII

Example

Run RNAfinder on a fungla mitocondrial genome to identify rns gene and capture the XML result in a file.

file=fungal_mt.fas
geneticcode=4
RNAfinder -m rns -g $geneticcode -d $file  -X - >result.xml

Contributing

Please see CONTRIBUTING and CONDUCT for details.

Credits

• All Contributors

License

GNU General Public License v3.0. Please see License File for more information.