NUPACK: help

Analysis Input

Analyze the thermodynamic properties of a dilute solution of interacting nucleic acid strands in the absence of pseudoknots.

Nucleic acid type:

Select RNA (default) or DNA for strand type. DNA/RNA hybrids are not allowed.

Temperature:

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.

Number of strand species:

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:

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 (if applicable):

Enter the total concentration of each strand species for calculations with maximum complex size greater than 1. Use the pull-down menu at right to specify units (default μM).

Advanced options:

Select among available energy models, select dangle treatments, specify salt concentrations, allow a class of pseudoknots, and specify additional ordered complexes.

Energy parameters:

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: 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.
Salt concentrations:

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).
Allow pseudoknots:

Include a class of pseudoknots in the structural ensemble (Dirks and Pierce, 2003; non-interacting RNA strands only).
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).

Compute time:

This order-of-magnitude estimate for the calculation time is updated as the job is specified. Jobs estimated to exceed a threshold are not accepted. NUPACK source code may be downloaded for non-commercial research purposes for use on a local machine.

Analyze:

Start the calculation.