Pseudoknot 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 5.39.

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


Current version of vs_subopt pseudoknot prediction program is now 5.39.


  • PLEASE NOTE: Numerous checking routines are installed to insure that the calculations make sense. These checking routines can cause the program to terminiate midway in a calculation and complain about perceived inconsistent data, data corruption, etc. If that happens, we're sorry, sometimes things go wrong. We think it is better to have a program that looks at a result and tries to decide if it makes sense, rather than have the program blindly calculate without thinking at all.
  • Warning: only sequences less than 400 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.

Eng. Intro

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]
Kuhn length: [nt]
minimum stem length: [bp]
typical values for Kuhn 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 judgement when you select a minimum stem length. This is not a black box!

search for pseudoknots
min linkage stem len: [bp]
leading edge length: [nt]

vs_subopt options:
maximum number of suboptimal structures: [#sos]
(1 - 40)
span of the free energy: [kcal/mol]
(0.5 - 1000.0 kcal/mol)
level of subopt struct: [zones]
(0 - 5 zones)

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]
effective Flory model
gamma: [n/a]
delta: [n/a]
nu1: [n/a]
nu2: [n/a]
Nc: [nt]
Rc: [nt]
include [Mg(H2O)6]2+ binding:

Contiguous stem connection parameters
#contiguous stems: [stems]