is a growing software suite for
the analysis and design of nucleic acid systems.
The NUPACK web application currently enables:
thermodynamic analysis of dilute solutions of interacting nucleic acid strands
single-state and multi-state sequence design for interacting nucleic acid strands
evaluation, display, and annotation of equilibrium properties of a complex of nucleic acid strands
NUPACK algorithms are formulated in terms of nucleic acid secondary structure.
In most cases, pseudoknots are excluded from the structural ensemble.
You are welcome to use NUPACK for your research. Please cite
NUPACK algorithms and the NUPACK web application appropriately.