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.

In the upper triangular region, a dot in row i and column j represents a base pair between the i^th and j^th 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, where p is the maximium percent deviation from 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).

Image resolution - gif files

The default value of 72 pixels per inch (Low) gives images that are very good for relatively short sequences. Longer sequences with complicated folds require higher resolution. The resolution option now computes gif images faster than before using custom software that in turn uses Bradley Sherman's tgd package which itself is based on Tom Boutell's gd gif-manipulating library.

Structure format

The PostScript and gif plots of secondary structure have 2 formats. In the first format, individual bases are shown and base pairs are depicted by colored dots. This is the "Bases" option. Otherwise, only an outline of the secondary structure is drawn, and base pairs become colored line segments. This is the "Outline" option. The default "Automatic" option draws bases when sequence length is less than 800, and an outline otherwise.

Structure numbering frequency

Individual structures are numbered, starting at some number N, and continuing with every multiple of N. When N=0, there is no structure numbering. If the user does not choose a value, it will be taken from the table below.

*Default numbering increment for structures.*
Sequence length	Numbering increment
1-50	10
51-300	20
> 300	50

Structure rotation

Plotted structures may be rotated through a user selected angle (in degrees). The default value is 0, and entries between ą360 are acceptable. The default value of 0 always places a closing stem in a vertical orientation, with the closing base pair at the bottom.

Structure annotation

Individual structures may be annotated using colored base characters, colored dots, or both. The annotation is based on either p-num or ss-count information. The color scheme is given in here. ss-count coloring follows the reverse scheme as p-num coloring. (red: most likely to be single stranded; high value of ss-count) See article by Zuker and Jacobson.

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.

*Default window parameters depending on sequence length. The user is encouraged to experiment with this parameter.*
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

Maximum distance between paired bases

If this parameter is set to max, then a base pair between bases numbered i to j will not be allowed if j-i > max. In a sequence of 1000 nucleotides, setting max to 50, for example, will force the server to compute foldings involving only short range base pairs. Please note that in circular sequences, a base pair i.j will be disallowed if and only if min{j-i,N+i-j} > max. This takes into account the circular nature of the molecule.

ss-count

ss-count is the propensity of a base to be single stranded, as measured by the number of times it is single stranded in a group of predicted foldings. The ss-count file gives the number of predicted foldings on the first line. The i^th subsequent line contains i and the number of foldings in which the i^th base was single stranded. The plotting option gives plots of ss-count values averaged over a user selected window.