DNA mfold server : 1996-2008, Michael Zuker, Rensselaer Polytechnic Institute
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This web server uses mfold (version 3.2) by Zuker and Turner. Users are requested to cite:

M. Zuker
Mfold web server for nucleic acid folding and hybridization prediction.
Nucleic Acids Res. 31 (13), 3406-15, (2003)
[Abstract] [Full Text] [Supplementary Material] [Additional Information]

The free energies used are from the laboratory of John SantaLucia Jr.
An appropriate citation for these energy rules is
SantaLucia, JJr (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA 95, 1460-1465. (Abstract)

For the salt correction, please cite:
Peyret, N. (2000) Prediction of Nucleic Acid Hybridization: Parameters and Algorithms PhD dissertation, Wayne State University, Department of Chemistry, Detroit, MI

* Related servers.
RNA mfold server.
D INAMelt  Full melting profile prediction for nucleic acids.
Quikfold server. Fold many short RNA or DNA sequences at once.
Zipfold server. Compute minimum folding energies only for many RNA or DNA sequences.
Tm server. Compute minimum folding energies and Tm only for many RNA or DNA sequences.
Hybridizataion server. Compute energies and Tm for the hybridization of two RNA or DNA sequences.
*Enter a name for your sequence:

* Enter the sequence to be folded in the box.
All non-alphabet characters will be removed.
FASTA format may be used.

* Enter constraint information in the box at the right. (optional) You may:
  1. force bases i,i+1,...,i+k-1 to be double stranded by entering:
    F   i   0   k on 1 line in the constraint box.
  2. force consecutive base pairs i.j,i+1.j-1, ...,i+k-1.j-k+1 by entering:
    F   i   j   k on 1 line in the constraint box.
  3. force bases i,i+1,...,i+k-1 to be single stranded by entering:
    P   i   0   k on 1 line in the constraint box.
  4. prohibit the consecutive base pairs
    i.j,i+1.j-1, ...,i+k-1.j-k+1 by entering:
    P   i   j   k on 1 line in the constraint box.
  5. prohibit bases i to j from pairing with bases k to l by entering:
    P   i-j   k-l on 1 line in the constraint box.
* The DNA sequence is .
* Folding temperature (between 0° and 100° C)
* Ionic conditions:   [Na+]     [Mg++]  
    Units: M     mM     Correction type: Oligomer     Polymer
* Enter the percent suboptimality number.
* Enter an upper bound on the number of computed foldings.
* Enter the window parameter if you wish.
* Enter the maximum distance between paired bases if you wish.

* Your job can be processed while you wait (the default) or can be submitted for batch processing by pressing the button below. In this case, you will be notified at a later time that the job is finished. Please enter your E-mail address in the window below.

Current limits: 800 bases for an immediate job, 6000 for batch.

* Select:     job for:
* Choose image width for png & jpg files:   Small:   Regular:   Medium:   Large:   XLarge:   Huge:
* Choose structure format:    Automatic:     Bases:     Outline:
* Grid lines in energy dot plot:    On:     Off:
* Choose structure draw mode:     .
* Choose base numbering frequency:     .
* Choose sequence numbering offset:     .
* Choose regularization angle (in degrees):        (Not used if 0.)
* Choose structure rotation angle (in degrees):   
* Choose structure annotation:    None:     p-num:     ss-count:     high-light:
    Enter high-light regions(s):  
Download the old mfold software (version 3.2) if you insist, or
download the much better UNAFold package.
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