Design Input
Design sequences for one or more strands intended to adopt an unpseudoknotted
target secondary structure at equilibrium.
Select RNA (default) or DNA for strand type. DNA/RNA hybrids
are not allowed.
Enter the temperature (default 37 °C).
The number of independent sequence designs to perform.
Enter the target secondary structure in
dot-parens-plus notation (each unpaired base is represented by a dot,
each base pair by matching parentheses, and each nick between strands by
a plus). Target structures must be connected and free of pseudoknots.
For example:
..(((...((((((..+.)))))).((((....)))))))
yields:
If a valid target structure is entered,
a visual preview is provided. Each base is shaded according to sequence
constraints specified under Advanced options:
A = green,
U/T = red,
G = black,
C = blue,
all others = gray.
Select among available energy models, specify dangle
treatments, specify salt concentrations, specify sequence constraints,
and define pattern prevention requirements.
-
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 user-defined 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).
-
Specify sequence constraints starting at the 5' end using
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 |
-
Specify patterns to be prevented in the designed sequences.
Enter one pattern per line using standard nucleic acid codes (depicted
above for RNA; T replaces U for DNA). No design will be produced
if the sequence constraints cannot be satisfied. Example patterns:
AAAA, CCCC, GGGG, UUUU, KKKKKK, MMMMMM, RRRRRR, SSSSSS, WWWWWW, YYYYYY.
Enter your email address for notification of job completion (required for long jobs).
Start sequence optimization.
