miRPV: An automated pipeline for miRNA Prediction and Validation in silico

miRPV is an Automated tool that allows users to predict and validate microRNA from genome/gene sequence.

miRPV Features:

• predict novel pre-miRNA from any given sequence
• predict secondary structure stability
• Predict authentic pre-miRNA
• predict novel mature miRNA
• Predict the novel miRNA target

Getting Started with miRPV

The installation has been tested on Ubuntu 18.04. If it has to be installed 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

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

cd miRPV

2) Install 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 root permission to install the following packages please provide it when asked.

HairpIndex, cowsay, enscript, dailog, build-essential, manpages-dev

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

5) Follow the on-screen guide
MATLAB Compiler Runtime (MCR) is used to Extract miRNA features, as it is Matlab code. Suppose it does not install via install.sh script install it separately from the Software directory.

Usage

Once all the tools and dependence are installed correctly, Activate Conda environment and run from the miRPV folder.

conda activate miRPV

bash miRPV.sh

Provide the project name.
* Give the input query fasta input (keep the fine in the miRPV directory).
* When asked to select the target prediction, select "Yes" or "NO."
* miRPV will ask to provide a reference sequence if the target prediction is selected. Keep the reference sequence in the miRPV folder and enter the name of the reference sequence in the terminal.
* After successful analysis, the results are saved in the output directory with the project name.

Troubleshoot installation:

If there is any issue in installation, please check the failed package log, install the dependencies, and run again.

conda install Perl-cpan-shell

Getopt::Long

conda install Perl-getopt-long

threads

conda install Perl-threaded

threads::shared

conda install Perl-mce-shared

CWD (CPAN)

conda install Perl-pathtools

or

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 

or

g77 -o ct2out ct2out.f

cp ct2out /bin/

If you need to know more, please contact on :

http://slsdb.manipal.edu

mlsc@manipal.edu