NUPACK: Analysis and design of nucleic acid systems

Abstract

The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. The NUPACK web server () 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.