dsRNAscan

dsRNAscan is a bioinformatics tool for genome-wide identification of double-stranded RNA (dsRNA) structures. It uses a sliding window approach to detect inverted repeats that can form dsRNA secondary structures, with support for G-U wobble base pairing and ML-based scoring.

Browse human genome results at dsrna.chpc.utah.edu

Install

pip install dsrnascan

Linux and macOS, Python 3.8+ (Windows: use WSL). If ViennaRNA fails via pip, install it with conda: conda install -c bioconda viennarna

Usage

# Basic scan (defaults: -w 10000 -s 500 --score 75 -c 4)
dsrnascan input.fasta

# Scan a region
dsrnascan genome.fasta --only_seq chr21 --start 33455482 --end 33655482

# Faster fold (~99% identical results)
dsrnascan genome.fasta --banded -c 8

# Settings used for the human dsRNAome resource
dsrnascan genome.fasta --v1

Run dsrnascan --help for all options.

Output

• *_merged_results.txt: one row per dsRNA with coordinates, einverted score, RNAduplex fold, structure and ML scores
• *.bedpe: paired arm coordinates (default)
• *.gff3: arms as linked features for IGV (--format gff3 or both)
• *.bp: base-pair arcs for IGV

Browse Results

# Interactive viewer with Forna RNA structure visualization
dsrna-browse results_directory/

# With RNA editing site annotations (BED or GFF3)
dsrna-browse results_directory/ --editing-file editing_sites.bed

Citation

If you use dsRNAscan, please cite:

dsRNAscan maps human dsRNAome, revealing conservation, intermolecular dsRNA, and correlates of ADAR dependency. Molecular Cell (2026). https://doi.org/10.1016/j.molcel.2026.08.001

License

GNU General Public License v3.0 - see LICENSE. Issues: GitHub Issues

Acknowledgments

• EMBOSS einverted (search) and ViennaRNA duplexfold (folding), both reimplemented in dsRNAscan's compiled engine