Pairfold [1] is a simple extension of the dynamic programming algorithm for predicting pseudoknot-free secondary structures of RNA by Zuker et al. [2]. This algorithm uses the nearest neighbourhood thermodynamics model. For RNA, PairFold uses the thermodynamics parameters by Turner Lab [3]. For DNA, it uses the thermodynamic parameters by SantaLucia Lab [4].

References

[1] M.Andronescu, Algorithms for predicting the secondary structure of several RNA/DNA sequences, MSc Thesis, Chapter 3, to appear.

[2] M. Zuker, D.H. Mathews & D.H. Turner, Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide In RNA Biochemistry and Biotechnology, J. Barciszewski & B.F.C. Clark, eds., NATO ASI Series, Kluwer Academic Publishers, (1999)

[3] Serra, M.J., Turner, D.H., & Freier, S.M. 1995. Predicting thermodynamic properties of RNA. Meth. Enzymol., 259, 243-261.

[4] SantaLucia, JJr (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA 95, 1460-1465.

Links

Michael Zuker's Web Page
Turner Group
John SantaLucia Lab