Name: Enter a name for your job.
Model: The default model calculates a partition function for each species at each temperature. You may choose instead to use only the minimum energy structure at each temperature, or to perform a two-state calculation for each species.
Temperature range: Each species is considered at Tmin°C, Tmin+Tinc°C, ..., Tmax°C. Depending on the values chosen, the highest temperature may be less than Tmax; it will always be in the range (Tmax-Tinc, Tmax].
NA type: Choose whether to interpret sequences as DNA (the default) or RNA.
Initial concentrations: Enter the initial concentrations of each sequence, in moles per liter.
Salt concentrations: For DNA rules only, enter the concentrations of Sodium and Magnesium ions. Oligomer mode is the default; if polymer mode is chosen, [Mg++] is ignored.
Advanced options: The "Activate filters" option removes base pairs that must be isolated, and ignores all structures with only one base pair. The "Energy only" option causes the calculation of probabilities to be skipped; this is significantly faster but prevents the computation of extinctions.
Exclude species: One or more species (folded A, folded B, hybridized A-A, hybridized B-B) may be excluded from consideration. Excluding a species that is known to be unimportant speeds up the computation. Note that the A-B heterodimer cannot be excluded.
Enthapy/entropy for single strands: Enter the fraction of ensemble enthalpy to be used as the enthalpy of unfolded single strands. If desired, adjust the melting temperature used to determine the corresponding entropy.
Email address: If you enter a valid email address here, you will be notified by email when your job is ready.
Sequences: Enter one or more sequences, in 5'-to-3' order, separated by semicolons. FASTA format is also accepted, in which case semicolons should not be used. The letters 'A', 'C', 'G', 'T' and 'U' are recognized as the corresponding nucleotides. (Us are converted to Ts for DNA and vice versa for RNA.) All other letters are treated as unknown nucleotides; such unknowns are not permitted to form base pairs. All non-alphabetic characters are stripped out prior to processing.
Energy Rules: Choose whether to interpret sequences as DNA (the default) or RNA. Enter a hybridization temperature in °C. (The new version 3.0 RNA rules are fixed at 37°C.) For DNA rules only, enter the concentrations of Sodium and Magnesium ions. (Salt conditions for RNA are fixed at [Na+] = 1 M and [Mg++] = 0 M.) Oligomer mode is the default; if polymer mode is chosen, [Mg++] is ignored.
Where applicable, "RNA" or "4.0" means the newest energy rules, and "RNA2" or "2.3" means the original RNA rules from mfold.
Sequence Type: Choose whether the molecules are linear or circular. (Linear molecules and circular molecules may not be folded in the same job.)
Structures: The server will generate structures with free energies within the specified percentage of the minimum free energy. The window size is a non-negative integer that affects how many structures are computed and how different they are — a larger window size means fewer structures with more differences among them. The maximum number of structures may also be limited if desired.
Maximum base pair distance: If specified, only allows pairing between bases within a certain distance of one another.