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Published January 15, 2011 | public
Journal Article

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 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.

Additional Information

© 2010 Wiley Periodicals, Inc. Received 4 April 2009; Accepted 10 May 2010; First published: 17 November 2010. The authors W. Yardley, N. Near-Ansari, and C. Schmutzer for technical support in deploying the NUPACK server, M. O'Connell for programming assistance, and V.A. Beck, J.D. Bishop, H.M.T. Choi, E. Franco, L.M. Hochrein, P.W.K. Rothemund, M. Schwarzkopf, J.B. Sternberg, S. Venkataraman, J.R. Vieregg, E. Winfree, P. Yin, and D.Y. Zhang for comments and testing. Contract/grant sponsor: National Science Foundation (The Molecular Programming Project); contract/grant number: CCF-0832824 , CHE-0533064, DMS-0506468. Contract/grant sponsor: The National Institutes of Health; contract/grant number: P50 HG004071. Contract/grant sponsor: The Ralph M. Parsons Foundation. Contract/grant sponsor: Beckman Institute at Caltech.

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