UNAFold (Unified Nucleic Acid Folding & Hybridization Package) is an integrated collection of programs that simulate folding, hybridization, and melting pathways for one or two single-stranded nucleic acid sequences. 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 (C(p)), and mole fractions of different molecular species are computed as a function of temperature.
mfold has been replaced by UNAFold.Although UNAFold will install without mfold_util, the sir_graph and boxplot_ng programs from the mfold_util package are required in order to obtain structure plots and dot plots from UNAFold. Install mfold_util before installing UNAFold. Versions 3.4 and higher of mfold contains all of the non-interactive programs in mfold_util, so a separate download is not required.
“FISHtrees” is a software program:
1) to parse copy numbers of multiple Fluorescence In Situ Hybridization (FISH) probe signals in a single-cell assay;
2) to analyze probe signals across multiple single-cell assays in a patient data file;
3) to model tumorigenesis as a tree of tumor progression paths for a given probe on a given patient data file;
4) to merge multiple tumorigenesis trees to represent multiple probes on a given patient data file;
5) to compute consensus multiple joint tumorigenesis trees representing multiple patient data files into a network as a graph of tumor progression pathways.
OligoWalk is an online sever calculating thermodynamic features of sense-antisense hybidization. It predicts the free energy changes of oligonucleotides binding to a target RNA. It can be used to design efficient siRNA targeting a given mRNA sequence.