LinearFold Web Server (beta)

Interactive demo
Add a sequence Paste or type your sequence here (length < 100,000):

Or upload a file in FASTA format:
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Arguments Beam size (1-200):
Constraints (one more line as structure constraints)
Zuker suboptimal structures

Available model(s)



Interactive demos for LinearPartition (using Vienna RNAfold thermodynamic model, Lorenz et al 2011, with parameters from Mathews et al 2004)

Preset demo for LinearFold

Example demos for 16S rRNA/23S rRNA/Group I Intron are available, compared with CONTRAfold v2.0 and Vienna RNAfold algorithms.

Please cite the following paper:

* Liang Huang, **He Zhang, **Dezhong Deng, Kai Zhao, Kaibo Liu, David Hendrix, and David H. Mathews (2019). LinearFold: Linear-Time Approximate RNA Folding by 5’-to-3’ Dynamic Programming and Beam Search. Bioinformatics, Volume 35, Issue 14, July 2019, Pages i295–i304. ISMB 2019
*Corresponding Author, **Equal Contribution.

Code: github (implemented by Kai Zhao, Dezhong Deng, He Zhang, and Liang Huang)
Web Demo designed by Kaibo Liu (

Some Other RNA Secondary Structure Prediction Web Servers
RNAfold (Vienna)   RNAstructure (Rochester)   CONTRAfold (Stanford)   Mfold (Albany)   CentroidFold (JBIC)