IRESfinder

IRESfinder is a python package for the identification of RNA internal ribosome entry site in eukaryotic cell, and it can be further used to search for the core IRES region.

Installation

The following software should be installed in your cluster or computer before running the lncScore.py.

Perl (version 5.10.1), https://www.perl.org/get.html.
Python (version 2.7.15), https://www.python.org/downloads/.
The scikit-learn module (version 0.17), http://scikit-learn.org/stable/install.html.

In most use cases the best way to install Python and scikit-learn package on your system is by using Anaconda(https://www.continuum.io), which is an easy-to-install free Python distirbution and includes more than 400 of the most popular Python packages. Anaconda includes installers(https://www.continuum.io/downloads) for Windows, OS X, and Linux.

Examples

Examples are provided in the 'examples' folder. Examples:

 Using IRESfinder with mode 0 (default), user can get a IRES score (probablity) for each sequence in .fa file,
 Command: python IRESfinder.py -f examples/example_mode_0.fa -o example_mode_0.result

 Using IRESfinder with mode 1, user can specific the region to be identified in the '>xx" line of the .fa file,
 Command: python IRESfinder.py -f examples/example_mode_1.fa -o example_mode_1.result -m 1

 Using IRESfinder with mode 2, user can search for the core IRES region by a sliding window (w: window size; s: step size),
 Command: python IRESfinder.py -f examples/example_mode_2.fa -o example_mode_2.result -m 2 -w 174 -s 50

Datasets

The IRES and non-IRES sequences in the training and testing datasets are provided in the 'dataset' folder.

Author

IRESfinder is developed by Jian Zhao (zhao_doctor@hotmail.com). For questions and comments, please contact Jian or submit an issue on github.

Reference

Zhao J., Wu J., Xu T., Yang Q., He J., and Song X.*, 2018. IRESfinder: Identifying RNA Internal Ribosome Entry Site in Eukaryotic Cell using Framed K-mer Features. 2018, Journal of genetics and genomics= Yi chuan xue bao, 45(7), p.403.