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

NUPACK: Analysis and design of nucleic acid systems.

Author information

1
Department of Bioengineering, California Institute of Technology, Pasadena, California 91125, USA.

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.

PMID:
20645303
DOI:
10.1002/jcc.21596
[Indexed for MEDLINE]

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