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Keywords:

  • RNA;
  • DNA;
  • complexes;
  • concentrations;
  • sequence design

Abstract

The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. The NUPACK web server (http://www.nupack.org) 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 nucleic acid strands.

NUPACK algorithms are formulated in terms of nucleic acid secondary structure. In most cases, pseudoknots are excluded from the structural ensemble. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010