We performed major hardware and software upgrades to the NUPACK web server on January 9, 2010. Please report any issues to support@nupack.org and thank you for your patience.
HCR hairpin
NUPACK is a growing software suite for the analysis and design of nucleic acid systems.

The NUPACK web server currently enables:

  • Analysis: thermodynamic analysis of dilute solutions of interacting nucleic acid strands.
  • Design: sequence design for complexes of nucleic acid strands intended to adopt a target secondary structure at equilibrium.
  • Utilities: evaluation, display, and annotation of equilibrium properties of a complex of interacting 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 the NUPACK web server for your research. Please cite NUPACK algorithms and the NUPACK web server appropriately.

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