Utilities
Evaluate, display, and annotate the equilibrium properties of an
ordered complex. The Utilities page accepts as input either sequence
information, structure information, or both, performing diverse
functions based on the information provided.
Select RNA (default) or DNA for strand type. DNA/RNA hybrids are
not allowed.
Update all calculations and graphics.
Enter the temperature (default 37 °C).
Specify a secondary structure in dotparensplus
notation (each unpaired base is represented by a dot, each base
pair by matching parentheses, and each nick between strands by a plus).
Structures must be connected and free of pseudoknots. For example:
..(((...((((((..+.)))))).((((....)))))))
yields:

Use the MFE structure as the specified structure.

Export structure information to the Design page, carrying
available sequence information as sequence constraints for the
redesign. This is useful when redimensioning duplex and loop
lengths in a target secondary structure while retaining sequence
information for a portion of the design.
Enter strand sequences with nicks betweem strands denoted “+”.
T's or U's are acceptable for both RNA and DNA and will be
appropriately converted. Each base can be any of the standard
nucleic acid codes (depicted below for RNA; T replaces U for DNA).
N  A,C,G,U 
R  A,G 
Y  C,U 
M  A,C 
K  G,U 
S  C,G 
W  A,U 
V  A,C,G 
H  A,C,U 
B  C,G,U 
D  A,G,U 

Position of the cursor within the ordered complex.

Export sequence information to the Analysis page (e.g., to
check for the formation of unintended ordered complexes in the
context of a dilute solution).
Depiction of the specified secondary structure in any
of a variety of formats.


Depict with ideal helical geometry (Aform helices for
RNA, Bform helices for DNA).

Depict bases as either circles or tick marks.

Shade each base according to: probability (the probability
that it adopts the depicted paired or unpaired state at equilibrium),
identity (A = green, U/T = red,
G = black, C = blue,
all others = gray), or none (all bases are black).

Annotate the drawing with any of: base letters,
base numbers, top text, bottom text.

Download an editable SVG file (without helicity) or a
PNG file (with helicity).

Edit the secondary structure layout (e.g., to eliminate overlaps).
Click the thumbnail for a larger version. Depicts
equilibrium basepairing probabilities for the ordered complex,
treating all strands as distinct. By definition, these data are
independent of concentration and of all other ordered complexes in
solution. The area and color of each dot scale with the equilibrium
probability of the corresponding base pair (probabilities below
0.001 are not depicted). With this convention, the plot is
symmetric, with the upper and lower triangles separated by a diagonal
line. The area and color of each dot in the column at right scale with
the equilibrium probability that the corresponding base is unpaired.
Select among available energy models, specify dangle
treatments, and specify salt concentrations.

For RNA, there are two parameter sets: (Serra and Turner,
1995; default) and (Mathews et al., 1999; valid only at 37 °C). For
DNA, there is one parameter set: (SantaLucia 1998).

None: no dangle energies are considered.
Some (default): a dangle energy is incorporated for
each unpaired base flanking a duplex (a base flanking two
duplexes contributes only the minimum of the two possible
dangle energies).
All: a dangle energy is incorporated for each base
flanking a duplex regardless of whether it is paired.

For RNA, the salt concentrations are 1.0 M Na^{+} and 0.0 M Mg^{++}.
For DNA, the userdefined salt concentrations can be set in the ranges
0.05 – 1.1 M Na^{+} (SantaLucia and Hicks, 2004; default 1.0 M) and
0.0 – 0.2 M Mg^{++} (Koehler and Peyret, 2005; default 0.0 M).
Download all data and plots for the utilities job as a single
compressed file.