Software for Nucleic Acid Folding and Hybridization
  • Nicholas R. Markham
  • Michael Zuker
Part of the Methods in Molecular Biology™ book series (MIMB, volume 453)


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

Key words:

RNA folding nucleic acid hybridization nucleic acid melting profiles (or DNA melting profiles) free energy minimization partition functions melting temperature. 



This work was supported, in part, by grants GM54250 and GM068564 from the National Institutes of Health and by a graduate fellowship to N.R.M. from RPI.


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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Nicholas R. Markham
    • 1
  • Michael Zuker
    • 2
  1. 1.Xerox Litigation ServicesAlbany
  2. 2.Mathematical Sciences and Biology DepartmentRensselaer Polytechnic InstituteTroy

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