This code from back in the day surveyed the human genome for potential microRNA sponges (decay elements).
It utilizes the miRBase database, https://www.mirbase.org, to identify segments in the genome that can potentially host multiple target sites for human microRNAs. Pipeline flow:
- Segmentation of the human genome according to size
- Prediction of the secondary structure of the segment using ViennaRNA toolkit, http://rna.tbi.univie.ac.at
- Parsing and annotation of dot-bracket notations for miRNA target sites at open secondary structures (bulges)
- Visualization of the secondary structures and seed sites using svg.
Example:
