References

mfold web server references

  • M. Zuker. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (13), 3406-3415, 2003.
    [Abstract] [Full Text] [Supplementary Material] [Additional Information]
  • A. Waugh, P. Gendron, R. Altman, J. W. Brown, D. Case, D. Gautheret, S. C. Harvey, N. Leontis, J. Westbrook, E. Westhof, M. Zuker & F. Major. RNAML: A standard syntax for exchanging RNA information. RNA 8 (6), 707-717, 2002.
    Note: Basis for RNAML output.
  • M. Zuker & A. B. Jacobson. Using Reliability Information to Annotate RNA Secondary Structures. RNA 4, 669-679, 1998.   [Abstract][Preprint]  Note: Explains color annotation of secondary structure.

UNAFold & mfold references

  • N. R. Markham & M. Zuker. UNAFold: Software for Nucleic Acid Folding and Hybridization. In Data, Sequence Analysis, and Evolution, J. Keith, ed., Bioinformatics: Volume 2, Chapter 1, pp 3-31, Humana Press Inc., 2008.  [Preprint]
  • M. Zuker, D. H. Mathews & D. H. Turner. Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide In RNA Biochemistry and Biotechnology, 11-43, J. Barciszewski and B. F. C. Clark, eds. , NATO ASI Series, Kluwer Academic Publishers, Dordrecht, NL, 1999.   [Preprint]
  • M. Zuker. Prediction of RNA Secondary Structure by Energy Minimization. In Computer Analysis of Sequence Data A. M. Griffin and H. G. Griffin eds. Methods in Molecular Biology, Humana Press Inc. , 267-294, 1994.  [Preprint]
  • J. A. Jaeger, D. H. Turner & M. Zuker. Predicting Optimal and Suboptimal Secondary Structure for RNA. In Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences, R. F. Doolittle ed. Methods in Enzymology 183, 281-306, 1990.
  • M. Zuker. On Finding All Suboptimal Foldings of an RNA Molecule. Science 244, 48-52, 1989.

Free energies for RNA

  • D. H. Mathews, J. Sabina, M. Zuker & D. H. Turner. Expanded Sequence Dependence of Thermodynamic Parameters Improves Prediction of RNA Secondary Structure J. Mol. Biol. 288, 911-940, 1999.
    Note: Basis for version 3 free energies.
  • A. E. Walter, D. H. Turner, J. Kim, M. H. Lyttle, P. Müller, D. H. Mathews & M. Zuker. Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc. Natl. Acad. Sci. USA 91, 9218-9222, 1994.
    Note: Basis for version 2.3 free energies.

RNA secondary structure prediction: Methods and Theory

  • D. H. Mathews, D. H. Turner & M. Zuker. RNA Secondary Structure Prediction. In Current Protocols in Nucleic Acid Chemistry S. Beaucage, D. E. Bergstrom, G. D. Glick, and R. A. Jones eds. , John Wiley & Sons, New York, 11. 2. 1-11. 2. 10, 2007.
  • D. H. Mathews, S. J. Schroeder, D. H. Turner & M. Zuker. Predicting RNA Secondary Structure. In The RNA World, R. F. Gesteland, T. R. Cech and J. F. Atkins eds., 3rd edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, Chapter 22, 2006.
  • D. H. Mathews & M. Zuker. Predictive Methods Using RNA Sequences. In Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, A. Baxevanis and F. Ouellette eds. , 3rd edition, John Wiley & Sons, New York, Chapter 7, 2005.
  • D. H. Mathews, M. D. Disney, J. L. Childs, S. J. Schroeder, M. Zuker & D. H. Turner. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci. USA 101 (19), 7287-7292, 2004.
  • M. Zuker & D. Sankoff. RNA Secondary Structures and their Prediction. Bull. Mathematical Biology 46, 591-621, 1984.
  • M. Zuker & P. Stiegler. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9, 133-148, 1981.

Some mfold & UNAFold applications

  • J. -M. Rouillard, M. Zuker & E. Gulari. OligoArray 2. 0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res. 31 (12), 3057-3062, 2003.
  • J. -M. Rouillard, C. J. Herbert & M. Zuker. OligoArray: Genome-scale oligonucleotide design for microarrays. Bioinformatics 18 (3), 486-487, 2002.