Automated miRDB-search of microRNA targets/seeds in mRNA sequences

This script implements a Selenium WebDriver to automate the access to miRDB - MicroRNA Target Prediction and Functional Study Database and search for microRNAs targets/seeds present in custom mRNA sequences.

Requirements

• Mozilla Firefox

  • You need to have Mozilla Firefox web browser installed and uptaded in your computer, which you can download here.

• Python

  • version 3

• Packages and libraries

  • geckodriver
  • openpyxl
  • biopython
  • selenium
  • pandas
  • beautifulsoup4

You can easily install packages and libraries by creating a conda environment with:

conda env create -f requirements.yml.

If so, don't forget to activate the environment with conda activate mirdb-search before running the script.

Running the script

python mirdb_custom_target_search.py [-h] [-c CUTOFF] [-v]
                                     inp out {Human,Rat,Mouse,Chicken,Dog}


positional arguments:
  inp                   Input FASTA file with target sequences
  out                   Name for output file
  {Human,Rat,Mouse,Chicken,Dog}
                        Species

optional arguments:
  -h, --help            show this help message and exit
  -c CUTOFF, --cutoff CUTOFF
                        Score cut-off <int> (default: 80)
  -v, --visible         Shows browser window during the process (default:
                        False)

Example:

./python mirdb-custom-target-search.py test_data.fa test Human

Output

sequence	score	seeds	mirna
NC_000010.11:87823625-87833625	96	10	hsa-miR-5692a
NC_000010.11:87823625-87833625	94	9	hsa-miR-3613-3p
...	...	...	...

References

• Weijun Liu and Xiaowei Wang (2019) Prediction of functional microRNA targets by integrative modeling of microRNA binding and target expression data. Genome Biology. 20:18.
• Nathan Wong and Xiaowei Wang (2015) miRDB: an online resource for microRNA target prediction and functional annotations. Nucleic Acids Research. 43(D1):D146-152.