viennarna

RNAblueprint library for uniform sampling of RNA sequences given structural and sequence constraints

Gibbs free energy evaluator for pseudoknotted RNA secondary structures

Github repository for the iGEM Team Heidelberg 2020 judging release software.

This repository has moved to https://codeberg.org/fncnt/librna-sys

Explainable microRNA precursor triage. Paste a human DNA or RNA sequence or an hg38 locus, fold it with ViennaRNA in your browser, and get a ranked shortlist of pre-miRNA-like hairpins with the evidence behind every score.

Physics-based 3D structure prediction for long circular RNA. Secondary-structure consensus, segmented multi-predictor folding, coarse-grained REMD + metadynamics, all-atom reconstruction. Ships a 2,013 nt all-atom model and the checks to re-derive its numbers. Team JLU-FBH, iGEM 2026.

Workflow for discovering and prioritizing locally conserved RNA secondary structure candidates from multiple sequence alignments

Codon optimization and structural modeling of perchlorate-reducing enzymes for Martian regolith bioremediation.

Computational Simulation of MicroRNA (miRNA) Biogenesis & RISC Loading

Various utilities for the RNAPlot program

A comprehensive GUI and CLI toolkit to predict RNA/DNA secondary structures using the ViennaRNA (RNAfold) engine and generate professional, artistic visualizations via RNArtistCore.

Comparative analysis of RNA secondary structure across 12 eukaryotic mRNAs — Master's thesis, University of Vienna

Analysis of how pre-mRNA secondary structure affects intron splicing efficiency. The project compares the effects of global RNA folding on gene output and the accessibility of the spliceosomal recognition sites on gene output. Based on the random intron library described by Schärfen et al. (2025).

Compute opening energy z scores of RNA

Retrospective computational evaluation of a 2,013 nt circRNA construct against the circDesign objectives, plus the verification layer that audits the audit: per-metric null models, exchangeability tests, pre-registered multi-objective dominance, and an explicit statement of where the construct is NOT optimal.

Family-held-out aptamer benchmark on two public HT-SELEX datasets, with experimental discrimination, a Markov generation baseline, and canonical-RNA structure ablation.

Desktop GUI tool for CRISPR/Cas9 guide RNA design — local gRNA search, Doench 16 scoring, secondary structure prediction with custom 2D plotting, interactive genomic map.

Quantum-assisted RNA secondary-structure prediction using QUBO, QAOA, ViennaRNA, Qiskit, encoding comparisons, and noise analysis.