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We describe an algorithm for designing the sequence of one or more interacting nucleic acid strands intended to adopt a target secondary structure at equilibrium. Sequence design is formulated as an optimization problem with the goal of reducing the ensemble defect below a user-specified stop condition. For a candidate sequence and a given target secondary(More)
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(More)
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