DNA folding form

Users of this service 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, Jr (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

Enter sequence name:    

Enter the sequence to be folded in the box below. 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.

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 make sure your E-mail address is correct in the window below.

Current limits: 800 bases for an immediate job, 9000 for batch.

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