UNAFold Software: Description and Man Pages
UNAFold is a comprehensive software package for nucleic acid folding and hybridization prediction. The name is derived from "Unified Nucleic Acid Folding". Folding of single-stranded RNA or DNA, or hybridization between two single-strands, is accomplished in a variety of ways. Partition functions can be computed to derive base pair probabilities and stochastic samples of foldings or hybridizations. Energy minimization methods compute minimum free energy foldings or hybridizations, and can also compute suboptimal foldings that mimic the performance of the famous mfold software.
For melting simulations, the package computes not just melting temperatures, but entire melting profiles. UV absorbance at 260 nm, heat capacity change (Cp), and mole fractions of different molecular species are computed as a function of temperature. ITC (Isothermal Titration Calorimetry) and van't Hoff plots are also simulated.
The package runs on Unix and Linux platforms, as well as under Mac OS X and Windows. Images of secondary structures, hybridizations, and dot plots may be computed from raw UNAFold output using easily available auxiliary software. Similarly, melting profile plots can be created. These melting plots include experimental results if they are provided.
UNAFold 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.
UNAFold may be downloaded freely for academic and other non-commercial use. Commercial use requires a special license from RPI.