Calculate the partition function and base pairing probability matrix in addition to the minimum free energy (MFE) structure.

Predicts only the optimal secondary structure.

Apart from the canonical AU and GC pairs RNA frequently forms (weaker) GU pairs. Check this box to disallow GU at the end of helices.

Predicted structures can contain isolated base pairs (helices of length 1), which may be undesirable. Check this box to avoid such lonely pairs.

RNA molecule is treated to be circular. Since Vienna RNA package v. 1.7 this options is also valid for partition function folding.

Incorporate G–Quadruplex formation into the structure prediction algorithm

The energy parameters used in the calculation have been measured at 37C. Parameters at other temperatures can be extrapolated, but for temperatures far from 37C results will be increasingly unreliable.

Energy parameters have been measured at default NaCl concentration of about 1M. Use this box to rescale the paramters to different (usually smaller) salt concentrations.

Energy correction for a few modified bases (mostly stacking energies) has been incorporated into the prediction algorithms. In your input sequence use the one-letter codes

I for inosine,
P for pseudouridine,
6 for N6-methyladenosie (m6A),
D for dihydrouridine,
7 for 7-deaza-adenosine (7DA) and
9 for purine (nebularine)

and check this box to let the prediction programs apply corrections whenever required.

Our webservices support handling of the tRNAdb one-letter-code annotation for modified bases in the input sequences. Usually, such modified bases are converted into their unmodified counterpart before they are passed to the prediction program

Keep modified bases known to stop reverse transcriptase from participation in any base pairs. Currently this includes the bases:
m1A m1G m22G m3U m3psi acp3U m3C Q

Do not convert modified bases supported by the prediction programs into their unmodified counterpart. Currently this includes the bases:
I P D m6A
Note, that the tRNAdb code for m6A (=) will be converted to 6.

Generates an interactive SVG-File displaying reliability information.

Colorize a secondary structure plot with reliability annotation from positional entropy and base-pairing probabilities.

A mountain plot represents a secondary structure in a plot of height versus position, where the height m(k) is given by the number of base pairs enclosing the base at position k. I.e. loops correspond to plateaus (hairpin loops are peaks), helices to slopes. Check this box to produce a PNG image with the mountain plot.