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NUPACK: Analysis and design of nucleic acid systems

โœ Scribed by Joseph N. Zadeh; Conrad D. Steenberg; Justin S. Bois; Brian R. Wolfe; Marshall B. Pierce; Asif R. Khan; Robert M. Dirks; Niles A. Pierce

Publisher
John Wiley and Sons
Year
2010
Tongue
English
Weight
68 KB
Volume
32
Category
Article
ISSN
0192-8651

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โœฆ Synopsis

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. ยฉ 2010 Wiley Periodicals, Inc. J Comput Chem, 2010

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