LinearX Webserver (Beta)

Interactive demo

LinearFold Web Server (beta)

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

Or upload a file in FASTA format

Arguments

Beam Size (LinearAlignment: 1 - 100)

Constraints (one more line as structure constraints)

Zuker suboptimal structures

? . ( ), each indicates a position for which the proper matching is unknown, unpaired, left or right parenthesis, respectively.

Available model(s)

LinearFold-C (using CONTRAfold v2.0 machine-learned model, Do et al 2006)

LinearFold-V (using Vienna RNAfold thermodynamic model, Lorenz et al 2011, with parameters from Mathews et al 2004)

LinearPartition

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 (liukaib@oregonstate.edu) & Apoorv Malik (malikap@oregonstate.edu)