http://mfold.rna.albany.edu/?

q=mfold
Structure Drawing Mode | Structure annotation | Energy dot plot | Exterior Loop
Image width - png & jpg files | Ionic Conditions | Structure numbering frequency
Max asymmetry of a bulge/interior loop | Max distance between paired bases
Max number of foldings | Max size of a bulge/interior loop | Structure format
Sequence numbering offset | Percent suboptimality | Regularization angle (in
degrees)
Structure rotation | ss-count | Window
Structure Drawing Mode
In natural mode, bases in a loop are placed on a circle, with a uniform distance
between them. (Exceptions are small bulge and interior loops. In these cases, the
two stems are coaxial.) Stems that branch from the loop are orthogonal to the
tangent of the circle at the closing base pair on the circle. This determines all of the
relative angles of helices. The structure plot may intersect itself. The untangle modes
determine relative angles to ensure non-ovelap. In addition, the loop fix extension
enlarges and/or modifies the shape of multi-branch loops to avoid drawing bases on
top of one another and to separate stems.
When "default" is chosen, structures with lengths up to 120 are drawn with natural
angles and otherwise with the loop fix untangle option. Structures may be
recomputed using different parameters after they have been computed.
Structure Drawing Mode | Structure annotation | Energy dot plot | Exterior Loop
Image width - png & jpg files | Ionic Conditions | Structure numbering frequency
Max asymmetry of a bulge/interior loop | Max distance between paired bases
Max number of foldings | Max size of a bulge/interior loop | Structure format
Sequence numbering offset | Percent suboptimality | Regularization angle (in
degrees)
Structure rotation | ss-count | Window
Structure annotation
Individual structures may be annotated using colored base characters, colored dots,
or both. Usually, the annotation is based on either p-num or ss-count information.
The color scheme is given 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. The "high-light" feature allows the user to specify
multiple ranges of bases, separated by commas (as in 3-9, 13-20, etc.). The high-
lighted regions will be in green, while the other regions will be drawn in black.
Structure Drawing Mode | Structure annotation | Energy dot plot | Exterior Loop
Image width - png & jpg files | Ionic Conditions | Structure numbering frequency
Max asymmetry of a bulge/interior loop | Max distance between paired bases
Max number of foldings | Max size of a bulge/interior loop | Structure format
Sequence numbering offset | Percent suboptimality | Regularization angle (in
degrees)
Structure rotation | ss-count | Window
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 dots represent the superposition of all possible
foldings within p% of ΔGmfe, the minimum free energy, where p is the maximium
percent deviation from ΔGmfe. Different colors are used to indicate varying levels of
suboptimality. The number of colors ranges from two to eight (the default). If n colors
are used, the first color indicates base pairs in optimal foldings. These base pairs are
also plotted in the lower left triangle (reversing row and column) for emphasis. The
remaining n-1 colors are used for base pairs in suboptimal foldings. If ΔGi.j is the
minimum of the free energies of all possible structures containing base pair i.j, and if
ΔGmfe+(k-2)pΔG/(n-1) < ΔGi.j ≤ ΔGmfe+(k-1)pΔG/(n-1), then color k is used for
base pair i.j, for 2 ≤ k ≤ n. When n is 8 (the default), the optimal base pairs are
colored in red and black colors base pairs that are least likely to form.
Structure Drawing Mode | Structure annotation | Energy dot plot | Exterior Loop
Image width - png & jpg files | Ionic Conditions | Structure numbering frequency
Max asymmetry of a bulge/interior loop | Max distance between paired bases
Max number of foldings | Max size of a bulge/interior loop | Structure format
Sequence numbering offset | Percent suboptimality | Regularization angle (in
degrees)
Structure rotation | ss-count | Window
Exterior loop
Single-stranded bases that are not in a hairpin, bulge, interior or multi-branch loop
are called "free bases". Similarly, a base pair at the end of a helix is called a "free
base pair" if it is not in a hairpin, bulge, interior or multi-branch loop. Free bases and
base pairs comprise the "exterior loop". The default option draws the exterior loop as
if it were a regular loop, except that the 5' and 3' ends are not joined (for linear
molecules). The "Flat" option places the exterior bases and base pairs on a straight
line. The helices associated with the external base pairs are all placed on the same
side of the line. The "Flat_Alt" option draws these helices on both sides of the line.
Odd numbered helices appear on one side and even number helices appear on the
other side.
Structure Drawing Mode | Structure annotation | Energy dot plot | Exterior Loop
Image width - png & jpg files | Ionic Conditions | Structure numbering frequency
Max asymmetry of a bulge/interior loop | Max distance between paired bases
Max number of foldings | Max size of a bulge/interior loop | Structure format
Sequence numbering offset | Percent suboptimality | Regularization angle (in
degrees)
Structure rotation | ss-count | Window
Image width - png & jpg files
The default value is 935 pixels (13 in / 33 cm). Longer sequences with complicated
folds require larger widths. Small sequences with simple folds require smaller widths.
Pdf and PostScripts images may be enlarged at will without loss in resolution. For
png and jpg format, the "domain" option should be used to plot selected parts of very
large foldings.
Structure Drawing Mode | Structure annotation | Energy dot plot | Exterior Loop
Image width - png & jpg files | Ionic Conditions | Structure numbering frequency
Max asymmetry of a bulge/interior loop | Max distance between paired bases
Max number of foldings | Max size of a bulge/interior loop | Structure format
Sequence numbering offset | Percent suboptimality | Regularization angle (in
degrees)
Structure rotation | ss-count | Window
Ionic conditions
The corrections for [Na+] and [Mg++] have been empirically derived. They are
currently being used only for DNA folding, where the conditions under which free
energy measurements were made, [Na+] = 1 M and [Mg++] = 0 M, are far from
reasonable physiological conditions.
Oligomer correction: [Na+] should be kept between 0.01 M and 1 M, and [Mg++]
should be no larger than 0.1 M. This correction is most likely valid for foldings that
result in stems of up to 20 base pairs, including bulges and interior loops. It is
certainly not valid for a long stretch of perfect Watson-Crick base pairs.
Polymer correction: [Mg++] must be 0. The combined effect of [Na+] and [Mg++] in
polymers is still not understood. This correction should be used when long stems
form. A "long stem" contains about 20 or more consecutive nucleotides that are base
paired or in bulge/interior loops .
Structure Drawing Mode | Structure annotation | Energy dot plot | Exterior Loop
Image width - png & jpg files | Ionic Conditions | Structure numbering frequency
Max asymmetry of a bulge/interior loop | Max distance between paired bases
Max number of foldings | Max size of a bulge/interior loop | Structure format
Sequence numbering offset | Percent suboptimality | Regularization angle (in
degrees)
Structure rotation | ss-count | Window
Stucture 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 lengthNumbering increment1-501051-30020> 30050
Maximum asymmetry of a bulge/interior loop
The upper bound on the asymmetry of a bulge/interior loop. This parameter is the
maximum size of a bulge loop. For interior loops, if the number of single-stranded
bases on the two sides are n1 and n2, then |n1 - n2| ≤ this limit.
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.
Structure Drawing Mode | Structure annotation | Energy dot plot | Exterior Loop
Image width - png & jpg files | Ionic Conditions | Structure numbering frequency
Max asymmetry of a bulge/interior loop | Max distance between paired bases
Max number of foldings | Max size of a bulge/interior loop | Structure format
Sequence numbering offset | Percent suboptimality | Regularization angle (in
degrees)
Structure rotation | ss-count | Window
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).
Maximium size of a bulge/interior loop
The upper bound on the total number of single-stranded bases that are allowed in a
bulge or interior loop. The default value is 30. The user may select any smaller
value.
Structure format
The PostScript, png & jpg 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 Drawing Mode | Structure annotation | Energy dot plot | Exterior Loop
Image width - png & jpg files | Ionic Conditions | Structure numbering frequency
Max asymmetry of a bulge/interior loop | Max distance between paired bases
Max number of foldings | Max size of a bulge/interior loop | Structure format
Sequence numbering offset | Percent suboptimality | Regularization angle (in
degrees)
Structure rotation | ss-count | Window
Sequence numbering offset
This number will be added to the base labels. If you wish, for example, your
sequence to begin with base N, then set OFFSET to N-1. The default is 0, or no
offset.
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/mol is rounded up to 1 kcal/mol. Similarly, an increment of more than 12.0
kcal/mol is rounded down to 12.0 kcal/mol.
Regularization angle (in degrees)
This non-negative number is not used if 0. If it is > 0 and if the drawing mode is
untangle (simple or loop fix), then angles between any two stems are always an
integral multiple of this regularization angle. Users are encouraged to experiment
with this (and other) parameters. Predicted secondary structures may be drawn over
and over again without refolding the sequence.
Structure Drawing Mode | Structure annotation | Energy dot plot | Exterior Loop
Image width - png & jpg files | Ionic Conditions | Structure numbering frequency
Max asymmetry of a bulge/interior loop | Max distance between paired bases
Max number of foldings | Max size of a bulge/interior loop | Structure format
Sequence numbering offset | Percent suboptimality | Regularization angle (in
degrees)
Structure rotation | ss-count | Window

Structure rotation
Plotted structures may be rotated through a user selected angle (in degrees). The
default value is 'auto', which means that the angle is chosen by the structure drawing
program, sir_graph. Otherwise, any positive or negative integer may be chosen for
counterclockwise or clockwise rotation, respectively.
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.
Structure Drawing Mode | Structure annotation | Energy dot plot | Exterior Loop
Image width - png & jpg files | Ionic Conditions | Structure numbering frequency
Max asymmetry of a bulge/interior loop | Max distance between paired bases
Max number of foldings | Max size of a bulge/interior loop | Structure format
Sequence numbering offset | Percent suboptimality | Regularization angle (in
degrees)
Structure rotation | ss-count | Window

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 lengthDefault window size0-29030-49150-1192120-1993200-2995300-
3997400-4998500-59910600-69911700-79912800-1199151200-199920> 199925