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NUPACK: Analysis and design of nucleic acid systems

Authors

  • Joseph N. Zadeh,

    1. Department of Bioengineering, California Institute of Technology, Pasadena, California, 91125
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    • These authors contributed equally to this work.

  • Conrad D. Steenberg,

    1. Department of Bioengineering, California Institute of Technology, Pasadena, California, 91125
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    • These authors contributed equally to this work.

  • Justin S. Bois,

    1. Department of Bioengineering, California Institute of Technology, Pasadena, California, 91125
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    • These authors contributed equally to this work.

  • Brian R. Wolfe,

    1. Department of Bioengineering, California Institute of Technology, Pasadena, California, 91125
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    • These authors contributed equally to this work.

  • Marshall B. Pierce,

    1. Department of Bioengineering, California Institute of Technology, Pasadena, California, 91125
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  • Asif R. Khan,

    1. Department of Bioengineering, California Institute of Technology, Pasadena, California, 91125
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  • Robert M. Dirks,

    1. Department of Bioengineering, California Institute of Technology, Pasadena, California, 91125
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  • Niles A. Pierce

    Corresponding author
    1. Department of Bioengineering, California Institute of Technology, Pasadena, California, 91125
    2. Department of Applied and Computational Mathematics, California Institute of Technology, Pasadena, California, 91125
    • Department of Bioengineering, California Institute of Technology, Pasadena, California, 91125
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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

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