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. 2011 Jan 15;32(1):170-3.
doi: 10.1002/jcc.21596.

NUPACK: Analysis and design of nucleic acid systems

Joseph N Zadeh  1 , Conrad D Steenberg, Justin S Bois, Brian R Wolfe, Marshall B Pierce, Asif R Khan, Robert M Dirks, Niles A Pierce
Affiliations

NUPACK: Analysis and design of nucleic acid systems

Joseph N Zadeh et al. J Comput Chem. .

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.

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