from http://www.bioinfo.rpi.edu/applications/mfold/

"The UNAFold web server is currenly an amalgamation of two existing web servers: mfold & DINAMelt. The aim of this web site is to integrate the existing servers and to expand by developing algorithms and software that will provide new services to the scientific community."

links from there to mfold and unifold seem to be dead

Here's an alternative site for the UNAfold server

http://www.introni.it/rnafold.html

"This server is based on UNAFold 3.6 software to predict secondary structures of single stranded RNA or DNA sequences."

Thanks Annemarie for your reply. Unfortunately, this website is not working as well. I submitted the sequence but it did not turn any results.

Sorry to hear that. These are some other RNA secondary structure prediction servers I have in my list - maybe one of those will fit your needs:

RNA Folding Servers

RNAfold WebServer

http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi

The RNAfold web server will predict secondary structures of single stranded RNA or DNA sequences. Current limits are 7,500 nt for partition function calculations and 10,000 nt for minimum free energy only predicitions.

The ViennaRNA Web Services

http://rna.tbi.univie.ac.at

This server provides programs, web services, and databases, related to our work on RNA secondary structures.

RNAstructure

https://rna.urmc.rochester.edu/RNAstructureWeb/

https://rna.urmc.rochester.edu/RNAstructureWeb/Servers/Predict1/Predict1.html

The Predict a Secondary Structure server combines four separate prediction and analysis algorithms: calculating a partition function, predicting a minimum free energy (MFE) structure, finding structures with maximum expected accuracy, and pseudoknot prediction. This server takes a sequence, either RNA or DNA, and creates a highly probable, probability annotated group of secondary structures, starting with the lowest free energy structure and including others with varied probabilities of correctness. Other structures are included because the minimum free energy structure may not be the correct one. Note that if SHAPE constraints are specified, the SHAPE constraints are applied to the probability annotated structures. In addition, a second group of SHAPE constrained, SHAPE annotated structures will be generated. This SHAPE structure group is distinct from the probability annotated structure group, and is not probability annotated itself.

RNAComposer

http://rnacomposer.cs.put.poznan.pl

The RNAComposer system offers a new user-friendly approach to the fully automated prediction of large RNA 3D structures. The method is based on the machine translation principle and operates on the RNA FRABASE database acting as the dictionary relating RNA secondary structure and tertiary structure elements.

RNAComposer works in two modes:

• interactive mode - allows to work on one RNA molecule of interest at a time; its use is limited up to 500 nt residues and results in a single 3D-RNA structure model. Input your RNA sequence and secondary structure (Example 1 and Example 2) or sequence only (Example 3). Example 3 is offered for introductory purposes.
• batch mode - is designed for large-scale automated modeling of RNA structures up to 500 nt residues, based on user-defined RNA secondary structures. As an input a set of up to 10 RNA sequences can be used. This mode is available only for registered users.

Thanks a lot. I will try them out.

You can try any of the following predictors:

• RNAfold (http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi)
• RNAstructure (https://rna.urmc.rochester.edu/RNAstructureWeb/Servers/Fold/Fold.html)
• LinearFold (http://linearfold.org/)
• SPOT-RNA from our lab (https://sparks-lab.org/server/spot-rna/)

All these predictors provide stanalone as well.

Sarah Sonbol

Hi Sarah,

you can still use MFOLD, its active again in UNAFOLD.

Link for MFOLD (http://www.unafold.org/mfold.php)

RNA folding form (http://www.unafold.org/RNA_form.php)

DNA folding form (http://www.unafold.org//DNA_form.php)

Cheers..

http://www.nupack.org/