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, 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 ±360 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 ith
subsequent line contains i and the number of foldings in which the
ith base was single stranded. The plotting option gives
plots of ss-count values averaged over a user selected window.