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Nucleic acid type:
RNA
DNA
Select RNA (default) or DNA for strand type. DNA/RNA hybrids are not allowed.
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). If pseudoknots are allowed, the maximum complex size is 1.
Allow pseudoknots:
Include a class of pseudoknots in the calculations. If checked, the maximum complex size is 1 and the nucleic acid type is RNA.
Number of strand species:
1
2
3
4
5
6
7
8
9
10
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.
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
Enter the initial concentration of the strand species. Use the pull-down menu at right to specify units (default μM).
Compute melt:
Perform the calculation over a range of temperatures.
Temperature:
C
Enter the temperature (in deg. C). If "Compute melt" is selected, the temperature minimum, increment, and maximum are requested.
Temperature lower bound:
C
Enter the temperature (in deg. C). If "Compute melt" is selected, the temperature minimum, increment, and maximum are requested.
Temperature increment:
C
Temperature upper bound:
C
Advanced options
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 would be "1 2 3 2".
RNA energy parameters:
mfold 2.3
mfold 3.0
For RNA, there are two parameter sets, mfold 2.3 (default) and mfold 3.0 (valid only at 37 deg. C). For DNA, the only option is mfold 2.3.
DNA energy parameters:
mfold 2.3
mfold 2.3
For RNA, there are two parameter sets, mfold 2.3 (default) and mfold 3.0 (valid only at 37 deg. C). For DNA, the only option is mfold 2.3.
Dangle treatment:
None
Some
All
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.
Email address:
Enter your email address for notification of job completion (required for long jobs).
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