Markham Nicholas R, Zuker Michael
Xerox Litigation Services, Albany, NY, USA.
Methods Mol Biol. 2008;453:3-31. doi: 10.1007/978-1-60327-429-6_1.
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 (C(p)), 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 .
UNAFold软件包是一组集成程序，可模拟一条或两条单链核酸序列的折叠、杂交和解链过程。该名称源自“统一核酸折叠”。单链RNA或DNA的折叠（二级结构）预测结合了自由能最小化、配分函数计算和随机抽样。对于解链模拟，该软件包计算的是完整的解链曲线，而不仅仅是解链温度。它会根据温度计算260nm处的紫外吸光度、热容变化（C(p)）以及不同分子种类的摩尔分数。该软件包可以在我们研究过的所有Unix和Linux平台上安装并运行，包括Mac OS X。二级结构、杂交和点阵图的图像可以使用通用格式进行计算。同样，在适当的时候会生成各种解链曲线图表。如果提供了实验结果，后者的图表中也会包含这些结果。该软件包由“命令行”驱动。底层的编译程序可以单独使用，也可以通过各种Perl脚本以特殊组合的方式使用。鼓励用户创建自己的脚本以补充软件包自带的功能。这个不断发展的软件可从http://www.bioinfo.rpi.edu/applications/hybrid/download.php下载。
