Bioinformatics pp 3-31
The UNAFold software package is an integrated collection of programs that simulate folding, hybridization, and melting pathways for one or two single-stranded nucleic acid sequences. The name is derived from “Unified Nucleic Acid Folding.” Folding (secondary structure) prediction for single-stranded RNA or DNA combines free energy minimization, partition function calculations and stochastic sampling. For melting simulations, the package computes entire melting profiles, not just melting temperatures. UV absorbance at 260 nm, heat capacity change (Cp), and mole fractions of different molecular species are computed as a function of temperature. The package installs and runs on all Unix and Linux platforms that we have looked at, including Mac OS X. Images of secondary structures, hybridizations, and dot plots may be computed using common formats. Similarly, a variety of melting profile plots is created when appropriate. These latter plots include experimental results if they are provided. The package is “command line” driven. Underlying compiled programs may be used individually, or in special combinations through the use of a variety of Perl scripts. Users are encouraged to create their own scripts to supplement what comes with the package. This evolving software is available for download at http://www.bioinfo.rpi.edu/applications/hybrid/download.php.
Key words:RNA folding nucleic acid hybridization nucleic acid melting profiles (or DNA melting profiles) free energy minimization partition functions melting temperature.
- 1.Bellman, R. E. (1957)Dynamic Programming. Princeton University Press, Princeton, NJ.Google Scholar
- 3.Waterman, M. S. (1978) Secondary structure of single-stranded nucleic acids, in (Rota, G.-C., ed.),Studies in Foundations and Combinatorics, Academic Press, New York.Google Scholar
- 6.Sankoff, D., Kruskal, J. B., eds. (1983)Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison. Addison-Wesley, Reading, MA.Google Scholar
- 7.Zuker, M. (1989) The use of dynamic programming algorithms in RNA secondary structure prediction, in (Waterman, M. S., ed.),Mathematical Methods for DNA Sequences. CRC Press, Boca Raton, FL.Google Scholar
- 8.Zuker, M. (1994) Prediction of RNA secondary structure by energy minimization, in (Griffin, A. M., Griffin, H. G., eds.),Computer Analysis of Sequence Data,. Humana Press, Totowa, NJ.Google Scholar
- 9.Zuker, M., Mathews, D. H., Turner, D. H. (1999) Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide, in (Barciszewski J., Clark, B. F. C., eds.),RNA Biochemistry and Biotechnology. Kluwer, Dordrecht.Google Scholar
- 21.Zhang, Y., Hammer, D. A., Graves, D. J. (2005) Competitive hybridization kinetics reveals unexpected behavior patterns.Bio-phys J 89, 2950–2959.Google Scholar
- 22.Kilgard, M. J. (1996)OpenGL Programming for the X Window System. Addison-Wesley, Boston.Google Scholar
- 23.Puglisi, J. D., Tinoco, I. Jr. (1989) Absorb-ance melting curves of RNA, in (Dahlberg, J. E., Abelson, J. N. eds.),RNA Processing Part A: General Methods. Academic Press, New York.Google Scholar