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Nucleic acid type:
RNA
DNA
Select RNA (default) or DNA for strand type. DNA/RNA hybrids are not allowed.
Temperature:
°C
Enter the temperature (default 37 °C). If "Compute melt" is selected, the minimum temperature, increment, and maximum temperature are requested.
Minimum temperature:
°C
Enter the temperature (default 37 °C). If "Compute melt" is selected, the minimum temperature, increment, and maximum temperature are requested.
Compute melt:
Analyze over a range of temperatures.
Increment:
°C
Maximum temperature:
°C
Number of strand species:
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
Select the number of distinct strand species from the pull-down menu (maximum of 10, default 1). If the same sequence is entered twice, it is considered to represent two distinct strand species.
Maximum complex size:
1
1
2
3
4
5
6
7
8
9
10
strand
All complex species up to this size will be considered in the calculation (maximum of 10, default 1).
Strand species
:
For each strand species, enter the name (default "Strand #") in the left field and the sequence in the right field. T's or U's are acceptable for both RNA and DNA and will be appropriately converted.
Concentration:
mM
μM
nM
pM
Advanced options
RNA energy parameters:
DNA energy parameters:
Serra and Turner, 1995
Mathews et al., 1999
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).
SantaLucia, 1998
SantaLucia, 1998
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).
Dangle treatment:
None
Some
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.
Allow pseudoknots:
Include a class of pseudoknots in the structural ensemble (Dirks and Pierce, 2003; non-interacting RNA strands only).
Na
+
:
1.0
M
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).
Mg
++
:
0.0
M
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).
Depict target structure:
Draw circles on the probability plot indicating the target structure
Specify additional ordered complexes:
Enter additional ordered complexes to be included in the calculation (augmenting those automatically specified based on the maximum complex size). Each line of space-separated integers describes one ordered complex. An example entry for an ordered complex containing one strand each of the first and third strand species and two of the second is "1 2 3 2".
Email address:
Enter your email address for notification of job completion (required for long jobs).
