Help with submitting sequences to this server
The following text is taken from the mfold server at RPI and explains some of the user defineable features of the mfold package.Percent suboptimality
If this number is set to p, then only foldings within p% from the minimum free energy will be computed. The energy dot plot contains the superposition of all possible foldings within p% of the minimum energy. An energy increment of less than 1 kcal/mole is rounded up to 1 kcal/mole. Similarly, an increment of more than 12.0 kcal/mole is rounded down to 12.0 kcal/mole.
Energy dot plot
In the upper triangular region, a dot in row i and column j represents a base pair between the ith and jth bases. The black dots represent all the optimal foldings. The colored, smaller dots represent the superposition of all possible suboptimal foldings within p% of the minimum free energy. The color ranges are red, blue and yellow; representing base pairs that are in foldings within p/3%, 2p/3% and p% of the minimum free energy, respectively. Thus the yellow dots represent base pairs that are least likely to form.
Maximium number of foldings
The upper bound on the number of foldings that are computed is not necessary. The folding algorithm automatically computes a selection of secondary structures within the prescribed energy increment and stops when no more sufficiently different foldings can be found. See also the definition of the window parameter (below).
Window
The window parameter controls how many foldings will be automatically computed and how different they will be from one another. It takes on positive whole number values. A smaller value of this parameter will usually result in more computed foldings that may be quite similar to one another. A larger value will result in fewer foldings that are very different from one another. If this parameter is not chosen by the user, a default value will be selected from the table below according to the sequence size.
| Sequence length | Default window size |
|---|---|
| 0-29 | 0 |
| 30-49 | 2 |
| 50-119 | 3 |
| 120-299 | 5 |
| 300-399 | 7 |
| 400-499 | 8 |
| 500-599 | 10 |
| 600-699 | 11 |
| 700-799 | 12 |
| 800-1199 | 15 |
| 1200-1999 | 20 |
| > 1999 | 25 |
How to use pairing constraints
Help with the results files and ZIP archives
If you continue to experience problems after consulting all available help pages please contact Dr Damian Purcell or the webmaster.