vsfold4.11:
RNA
Secondary Structure Prediction
Server
...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.

WARNING: you are using an old version of this program. The latest is here. This version of vsfold is 4.11.

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

News:

Nov. 1st 2005: the server acknowledges Tt characters as "U". _o_

Oct. 25th 2005: An email service is now available. Please enter your email address in the box below, and a URL link to your calculation will now be e-mailed to you. Calculated structure data will be saved for approximately 7 days.

Notes:

  • Warning: only sequences less than 250 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.
authors
contributors
sponsors
General information:
Seq. Name:
(no special
characters!!!)
e mail address:
(for email
service)
paste sequence here:
(only sequence part,
no comment, etc.)
Basic options:
temperature: [deg C]
persistence length: [nt]
minimum stem length: [bp]
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]
McKenzie-Moore-
Domb and Fisher model
t: [n/a]
delta: [n/a]
include [Mg(H2O)6]2+ binding:
Contiguous stem connection parameters
#contiguous stems: [stems]
free strand search dist: [nt]