help-quickfold

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.

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.