Nucleic acid type:
RNA DNA
Select RNA (default) or DNA for strand type.
Number of designs:
The number of sequences to design.
Target structure:
Input the target structure in dot-parens format. Pseudoknots are not allowed.

In dot-parens notation, each unpaired base is represented by a dot and each base pair is represented by matching parens. Strand breaks are denoted by "+". For example:

..(((...((((((..+.)))))).((((....)))))))

yields:
Preview:
When a valid secondary structure is entered for the target structure, a valid secondary structure drawing will be shown.
Temperature:
C
Enter the temperature (in deg. C).
Advanced options
RNA energy parameters:
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: 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.
Sequence constraints:
This field can be used to constrain base identities throughout the design. The user can input a general sequence into this field; all outputted designs will have the form. In addition to A,C,G,T/U the following nucleic acid codes can also be used:
NA,C,G,T/U
RA,G
YC,T/U
MA,C
KG,T/U
SC,G
WA,T/U
VA,C,G
HA,C,T/U
BC,G,T/U
DA,G,T/U
Prevented sequence patterns:
Enter sub-sequence patterns that should not appear in the designed sequences. In addition to A,C,G,T/U the following nucleic acid codes can also be used:
NA,C,G,T/U
RA,G
YC,T/U
MA,C
KG,T/U
SC,G
WA,T/U
VA,C,G
HA,C,T/U
BC,G,T/U
DA,G,T/U
Enter one sub-sequence per line. No design will be produced if the sequence constraints cannot be satisfied.
Email address:
Enter your email address for notification of job completion (required for long jobs).
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