Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY 14642, USA.
BMC Bioinformatics. 2010 Mar 15;11:129. doi: 10.1186/1471-2105-11-129.
To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence.
RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained.
The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at http://rna.urmc.rochester.edu/RNAstructure.html.
为了理解 RNA 序列的作用机制，必须了解其结构。此外，在设计小干扰 RNA 和反义 DNA 寡核苷酸时，靶 RNA 结构是一个重要的考虑因素。使用热力学进行 RNA 二级结构预测可用于提出有关 RNA 序列结构的假设。
RNAstructure 是一个用于 RNA 二级结构预测和分析的软件包。它使用热力学，并利用 Turner 小组最新的一组近邻参数。它包括二级结构预测方法（使用几种算法）、碱基对概率预测、双分子结构预测以及两个序列共有结构的预测。本贡献描述了该软件包的新扩展，包括可集成到其他程序中的 C++类库、用 JAVA 编写的用户友好图形用户界面以及新的 Unix 样式文本界面。用于 Microsoft Windows 的原始图形用户界面仍在维护中。
RNAstructure 的扩展使 RNA 二级结构预测更加用户友好。该软件包可从 Mathews 实验室主页下载，网址为 http://rna.urmc.rochester.edu/RNAstructure.html。
