Bioinformatics tool for exploring RNA-Protein interactions

Explore RNA-Protein interactions.

RNPFind is a bioinformatics tool. It takes an RNA transcript as input and gives a list of RNA binding protein (RBP) binding sites on the transcript as output.

Various output formats for representing the binding sites is supported.

Usage

Use rnpfind as either a command line tool or through the webtool.

Command line tool

The full docs are available here, but a quick example for installation and use is:

pip install rnpfind
rnpfind -f bed -o ./malat1-sites malat1

which installs rnpfind from the PyPi respository, and then invokes the program to generate binding sites for the gene malat1 in the bed file format in the directory ./malat1-sites.

Note that the tool will download large data files upon first invocation (around 6.4 GB). If the memory footprint is too much for you, the web tool is probably better for you.

Web tool

Visit the RNPFind website and the rest is pretty self-explanatory.

How does it work?

RNPFind collects its data from three main databases:

• ATTRACT
• RBPDB
• POSTAR

Each database stores binding sites of RBPs deduced through various methods, such as various experimental methods as well as computational methods. RBPDB and ATTRACT provide binding site patterns for RBPs, so we scan the input gene's sequence to deduce the binding sites. POSTAR stores experimentally deduced binding sites for the transcriptome for all RBPs, so we simply query.

Acknowledgements

This tool was produced at iYLab at CMUQ to help both my molecular biology research project as well as that of others in the lab. Originally a CLI tool that needed to be installed on the user's computer, it was made into a webapp later for ease of use and access.