NUPACK: Analysis and design of nucleic acid systems
Joseph N. Zadeh(California Institute of Technology), Conrad Steenberg(California Institute of Technology), Justin S. Bois(California Institute of Technology), Brian R. Wolfe(California Institute of Technology), Marshall B. Pierce(California Institute of Technology), Asif R. Khan(California Institute of Technology), Robert M. Dirks(California Institute of Technology), Niles A. Pierce(California Institute of Technology)
Cited by 1,788Open Access
Abstract
UNLABELLED: 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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