NUPACK: Analysis and design of nucleic acid systems

TLDR

The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. The NUPACK web server enables thermodynamic analysis of dilute solutions of interacting nucleic acid strands. NUPACK provides design tools for sequence design of complexes targeting a specified secondary structure, utilities for evaluating and visualizing equilibrium properties, and algorithms based on secondary structure that generally exclude pseudoknots. © 2010 Wiley Periodicals, Inc., J Comput Chem.

Abstract

Abstract 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. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010