NUPACK: Analysis and design of nucleic acid systems

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 co...

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Bibliographic Details
Published in:Journal of computational chemistry 2011-01, Vol.32 (1), p.170-173
Main Authors: Zadeh, Joseph N, Steenberg, Conrad D, Bois, Justin S, Wolfe, Brian R, Pierce, Marshall B, Khan, Asif R, Dirks, Robert M, Pierce, Niles A
Format: Article
Language:English
Subjects:
Acids
Algorithms
Analytical chemistry
Aqueous chemical equilibrium
complexes
concentrations
DNA
DNA - chemistry
Models, Molecular
Nucleic Acid Conformation
Nucleic Acids - chemistry
RNA
RNA - chemistry
sequence design
Software
Thermodynamics
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Summary: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.
ISSN:0192-8651
1096-987X
DOI:10.1002/jcc.21596