help

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.

Sequences: Enter two sequences, in 5'-to-3' order. 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. Currently sequences may be at most 50 bases long.

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.