RNA Secondary Structure Prediction — MFE Fold (Zuker / Turner)
Fold an RNA to its minimum-free-energy secondary structure — dot-bracket, MFE, base-pair list and an exportable arc diagram, without installing ViennaRNA.
🔒 Nothing you paste is logged or stored
Predicted, not measured
- How good is it?
- No held-out skill statistic is claimed for this implementation. The loop model omits terminal mismatches, dangling ends, coaxial stacking and special hairpins that ViennaRNA and RNAstructure include, so the MFE is a comparative estimate between candidates rather than a lab-grade absolute.
- Only valid for:
- a single strand up to 600 nt at a fixed 37 °C. No pseudoknots, no two-strand hybridisation, and no temperature dependence — a structure predicted here is not a structure at your annealing temperature.
- Fitted on:
- Turner nearest-neighbour free energies from optical melting experiments. The stacking table is identical in Turner 1999 and 2004; the loop-initiation tables here are a documented HYBRID of the two releases, with internal sizes 2-3 deliberately softened because there are no int11/int21 special-case tables.
Paste an RNA sequence (or DNA — it's treated as RNA) and fold it to its minimum-free-energy secondary structure. The engine is a from-scratch Zuker dynamic program using the Turner 1999 nearest-neighbor stacking free energies with length-based hairpin/bulge/internal-loop penalties and a linear multiloop model — the same algorithm class as RNAfold/mfold, implemented natively so it runs on any device with nothing to install. You get the dot-bracket structure, the estimated MFE, the base-pair list, and an arc diagram you can export. Because the loop energy model is simplified (no full terminal-mismatch/special-hairpin/coaxial-stacking tables and no pseudoknots), treat the MFE as a solid comparative estimate — great for comparing candidates or checking an oligo's self-structure — rather than a lab-grade absolute.
Working on a whole construct rather than one fold? Open SeqStudio — the full editor, with live feature annotation, plasmid maps, restriction and primer panels, undo/redo, multi-document tabs and GenBank / SnapGene import and export.
How to use the RNA Structure (MFE) tool
- 1Paste an RNA/DNA sequence (up to a few hundred nt) or load the tRNA example.
- 2Read the MFE, base-pair count and dot-bracket structure, and inspect the arc diagram (each arc is a base pair).
- 3Export the arc diagram, or copy the dot-bracket — and remember it's a simplified-model estimate, best used comparatively.
Frequently asked questions
What algorithm and energies does it use?
A Zuker minimum-free-energy dynamic program (the V/W/WM recursions) with Turner 1999 nearest-neighbor stacking free energies, length-based hairpin/bulge/internal-loop initiation penalties, a Ninio asymmetry term, and a linear multiloop model. It predicts one MFE structure and does not allow pseudoknots — standard for this class of tool.
How accurate is the MFE?
It's a good comparative estimate, not a lab-grade absolute. The loop energy model is deliberately simplified relative to a full ViennaRNA/mfold parameter set (no complete terminal-mismatch, special-hairpin, or coaxial-stacking tables), so absolute kcal/mol values will differ somewhat from those tools. It's well-suited to ranking candidates, checking whether a region tends to be structured, or evaluating an oligo's self-structure.
Why not just use ViennaRNA?
Use it when you need its full parameter set — this tool exists for the far more common case where you want one fold now, from a browser or an API call, with nothing to install and no cluster to queue on. It implements the same standard Zuker/Turner MFE method natively, so the structures and relative energies are directly comparable.
Is there a size limit?
Yes — folding is O(n³), so inputs are capped at a few hundred nucleotides to keep responses fast. Fold a specific region rather than a whole transcript.
Is my sequence stored, and can I use this from code?
No. Your sequence is used only to compute the fold and is never logged or stored. The rna_fold tool is available via the REST API and MCP server.
More
Guides
Related tools
Search a gene and get its exon/CDS structure, a druggability/disease/drug/trial/paper dossier, and a GTEx + Human Protein Atlas expression fingerprint — all in one page.
Test a gene list for enriched GO terms and Reactome pathways with hypergeometric p-values and BH-FDR correction.
Lay out PCR reactions on a 96-well plate and export a runnable Opentrons protocol or Echo picklist.