Secondary Structure Prediction
...where the folding landscape is always funnel shaped
The High Technology Research Center
Chiba Institute of Technology

Welcome(!) and thank you for your interest in this RNA secondary structure prediction server. The current folding program is version 4.23. If you wish to use the older version 4.11, please go to the following link.

Please feel free to contact the help desk if you have any specific questions.


_NEW_ May 27, 2015: The subopt version (vs_subopt) is now open.


  • Warning: only sequences less than 450 nt in length can currently be evaluated on this server. Anything longer will unfortunately be rejected.
  • Remember: Default values are changed only if you mark them.
  • Please read the [?] boxes before selecting special options
  • You are advised to use the "Jacobson-Stockmayer" if you are not familiar with the newer models that are offered. To begin with, try the default parameters.


General information:
Seq. Name:
(no special
e mail address:
(for email
paste sequence here:
(only sequence part,
no comment, etc.)

Basic options:
temperature: [deg C]
persistence length: [nt]
minimum stem length: [bp]
typical values for persistence length:
4-6 nt tRNA-like
6-9 nt functional RNA (& some riboswitches)
10 nt (& greater) rRNA and ribozyme-like
Note 1: With functional RNA and particularly with long sequences, it is better to use the MMDF model (or Flory if you are brave enough to try).
Note 2: Use good judgment when you select a minimum stem length. This is not a black box!

polymer model options
Jacobson-Stockmayer (standard parameters)
gamma: [n/a]
Flory solvent model
gamma: [n/a]
delta: [n/a]
B2: [nm^3/mol]
B3: [nm^6/mol^2]
epsilon: [n/a]
Domb and Fisher model (MMDF)
gamma: [n/a]
delta: [n/a]
include [Mg(H2O)6]2+ binding:

Contiguous stem connection parameters
#contiguous stems: [stems]
free strand search dist: [nt]