NUPACK: Analysis and design of nucleic acid systems

@article{Zadeh2011NUPACKAA,
  title={NUPACK: Analysis and design of nucleic acid systems},
  author={Joseph N. Zadeh and Conrad Steenberg and Justin S. Bois and Brian R. Wolfe and Marshall B. Pierce and Asif R. Khan and Robert M. Dirks and Niles A. Pierce},
  journal={Journal of Computational Chemistry},
  year={2011},
  volume={32}
}
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… 

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References

SHOWING 1-10 OF 16 REFERENCES

Thermodynamic Analysis of Interacting Nucleic Acid Strands

TLDR
This dynamic program is based on a rigorous extension of secondary structure models to the multistranded case, addressing representation and distinguishability issues that do not arise for single-stranded structures.

A partition function algorithm for nucleic acid secondary structure including pseudoknots

TLDR
An O(N5) dynamic programming algorithm is described, where N is the length of the strand, for computing the partition function and minimum energy structure over this class of secondary structures, to determine the probability of sampling the lowest energy structure, or any other structure of particular interest.

Paradigms for computational nucleic acid design.

TLDR
Surprisingly, the findings hold for a wide range of secondary structures and are robust to modest perturbation of the thermodynamic parameters used for evaluating sequence quality, suggesting the feasibility and ongoing utility of a unified approach to nucleic acid design as parameter sets are refined further.

An algorithm for computing nucleic acid base‐pairing probabilities including pseudoknots

TLDR
A method for computing base‐pairing probabilities starting from the output of this partition function algorithm based on the calculation of recursion probabilities that are computed by backtracking through the partitions function algorithm, applying a particular transformation at each step.

The thermodynamics of DNA structural motifs.

TLDR
This review presents the current parameter set available for making accurate DNA structure predictions and also points to future directions for improvement.

Predicting thermodynamic properties of RNA.

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.

TLDR
An improved dynamic programming algorithm is reported for RNA secondary structure prediction by free energy minimization and experimental constraints, derived from enzymatic and flavin mononucleotide cleavage, improve the accuracy of structure predictions.

Thermodynamic properties of DNA sequences: characteristic values for the human genome

TLDR
The results provide the first survey of typical and limiting thermodynamic values evaluated on a genomic scale and comprise useful 'rules of thumb' that are applicable to most technologies dependent upon DNA oligo design.

A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics.

  • J. SantaLucia
  • Chemistry, Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1998
TLDR
Six of the studies are actually in remarkable agreement with one another and explanations are provided in cases where discrepancies remain, and a single set of parameters, derived from 108 oligonucleotide duplexes, adequately describes polymer and oligomer thermodynamics.

Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers

TLDR
An implementation of McCaskill's algorithm for computing the base pair probabilities of an RNA molecule for massively parallel message passing architectures is presented and applications to complete viral genomes are discussed.