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.
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.
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.
Start the calculation.