miRPV: An Automated Pipeline for miRNA Prediction and Validation In Silico

miRPV is an automated tool that enables users to predict and validate microRNAs from genome/gene sequences.

miRPV Features:

• Predict novel pre-miRNA from any given sequence
• Predict secondary structure stability
• Predict authentic pre-miRNA
• Predict novel mature miRNA
• Predict novel miRNA targets

Getting Started with miRPV

The installation has been tested on Ubuntu 18.04. If you wish to install it on another platform, please use the virtual machine image preinstalled with miRPV.

System Requirement

• CPU: AMD64 (64bit)
• Memory: 2Gb RAM
• Storage: 5Gb
• Ubuntu 18.04

INSTALLATION

1. Clone this repository. If git is not installed, run:

sudo apt install git

Then, clone the repository:

git clone https://github.com/pradyumnasagar/miRPV.git

And navigate to the miRPV directory:

cd miRPV

2. Install the dependencies:

sudo apt install -y cowsay enscript dialog build-essential manpages-dev curl gfortran

3. Create a conda environment:

conda create -n miRPV python=2

conda activate miRPV

4. Run the installation script. The installer will ask for root permission to install the following packages. Please provide it when prompted:

• HairpIndex
• cowsay
• enscript
• dialog
• build-essential
• manpages-dev

bash install.sh -p  <path of miRPV folder>

5. Follow the on-screen guide. If MATLAB Compiler Runtime (MCR) is not installed via the install.sh script, please install it separately from the Software directory.

Usage

Once all the tools and dependencies are installed correctly, activate the Conda environment and run miRPV from the miRPV folder:

conda activate miRPV

bash miRPV.sh

• Provide a project name and input query fasta input (keep the file in the miRPV directory).
• When asked to select the target prediction, select "Yes" or "No."
• If the target prediction is selected, miRPV will ask for a reference sequence.
• Keep the reference sequence in the miRPV folder and enter its name in the terminal.
• After successful analysis, the results are saved in the output directory with the project name.

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Troubleshoot installation:

If there is an issue with the installation, please check the failed package log, install the dependencies, and try again:

conda install Perl-cpan-shell
conda install Perl-getopt-long
conda install Perl-threaded
conda install Perl-mce-shared
conda install Perl-pathtools

Alternatively, you can install CWD from CPAN

perl -MCPAN -e 'install CWD'

File::chdir

conda install Perl-file-chdir

UNAFold

conda install -c bioconda oligoarrayaux

gfortran

conda install -c anaconda gfortran_linux-64

libsvm

conda install libsvm

ct2out

gfortran ct2out.f -o ct2out 

cp ct2out /bin/

If you require more assistance, please contact:

http://slsdb.manipal.edu

[email protected]