mfold server: 1995-2008, 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]

and

D.H. Mathews, J. Sabina, M. Zuker & D.H. Turner
Expanded Sequence Dependence of Thermodynamic Parameters Improves Prediction of RNA Secondary Structure
J. Mol. Biol. 288, 911-940 (1999)

The folding temperature is fixed at 37°. You may still fold with the older version 2.3 RNA parameters, which allow the temperature to be varied.   RNA mfold version 2.3 server.

Yellow ball The DNA mfold server.
Quikfold server. Fold many short RNA or DNA sequences at once.

Yellow ballEnter a name for your sequence:    

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

Yellow ball 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.
Yellow ball The RNA sequence is .
Yellow ball Folding temperature is fixed at 37°.  
Yellow ball Ionic conditions: 1M NaCl, no divalent ions.
Yellow ball Enter the percent suboptimality number.  
Yellow ball Enter an upper bound on the number of computed foldings.  
Yellow ball Enter the window parameter if you wish.  
Yellow ball Enter the maximum interior/bulge loop size  
Yellow ball Enter the maximum asymmetry of an interior/bulge loop  
Yellow ball Enter the maximum distance between paired bases if you wish.  

Yellow ball 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. If you select a batch job, please make sure your E-mail address is correct in the window below.
Yellow ball Select: job for:  
Yellow ball Choose image width for png & jpg files:   Small:   Regular:   Medium:   Large:   XLarge:   Huge:
Yellow ball Choose structure format:    Automatic:     Bases:     Outline:
Yellow ball Grid lines in energy dot plot:    On:     Off:
Yellow ball Choose structure draw mode:     .
Yellow ball Choose exterior loop type:     .
Yellow ball Choose base numbering frequency:     .
Yellow ball Choose sequence numbering offset:     .
Yellow ball Choose regularization angle (in degrees):        (Not used if 0.)
Yellow ball Choose structure rotation angle (in degrees):   
Yellow ball Choose structure annotation:    None:     p-num:     ss-count:     high-light:
    Enter high-light regions(s):  
Current limits: 800 bases for an immediate job, 6000 for batch.
Download mfold version 3.2.
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