NUPACK: Design input

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:

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:

N	A,C,G,T/U
R	A,G
Y	C,T/U
M	A,C
K	G,T/U
S	C,G
W	A,T/U
V	A,C,G
H	A,C,T/U
B	C,G,T/U
D	A,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:

N	A,C,G,T/U
R	A,G
Y	C,T/U
M	A,C
K	G,T/U
S	C,G
W	A,T/U
V	A,C,G
H	A,C,T/U
B	C,G,T/U
D	A,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).