Department of Computer Science, Ben-Gurion University, 84105 Beer Sheva, Israel.
BMC Bioinformatics. 2011 Aug 3;12:319. doi: 10.1186/1471-2105-12-319.
RNAexinv is an interactive java application that performs RNA sequence design, constrained to yield a specific RNA shape and physical attributes. It is an extended inverse RNA folding program with the rationale behind that the generated sequences should not only fold into a desired structure, but they should also exhibit favorable attributes such as thermodynamic stability and mutational robustness. RNAexinv considers not only the secondary structure in order to design sequences, but also the mutational robustness and the minimum free energy. The sequences that are generated may not fully conform with the given RNA secondary structure, but they will strictly conform with the RNA shape of the given secondary structure and thereby take into consideration the recommended values of thermodynamic stability and mutational robustness that are provided.
The output consists of designed sequences that are generated by the proposed method. Selecting a sequence displays the secondary structure drawings of the target and the predicted fold of the sequence, including some basic information about the desired and achieved thermodynamic stability and mutational robustness. RNAexinv can be used successfully without prior experience, simply specifying an initial RNA secondary structure in dot-bracket notation and numerical values for the desired neutrality and minimum free energy. The package runs under LINUX operating system. Secondary structure predictions are performed using the Vienna RNA package.
RNAexinv is a user friendly tool that can be used for RNA sequence design. It is especially useful in cases where a functional stem-loop structure of a natural sequence should be strictly kept in the designed sequences but a distant motif in the rest of the structure may contain one more or less nucleotide at the expense of another, as long as the global shape is preserved. This allows the insertion of physical observables as constraints. RNAexinv is available at http://www.cs.bgu.ac.il/~RNAexinv.
RNAexinv 是一个交互式的 Java 应用程序，用于执行 RNA 序列设计，其设计受到特定 RNA 形状和物理属性的限制。它是一个扩展的反向 RNA 折叠程序，其基本原理是生成的序列不仅要折叠成所需的结构，而且还应该表现出有利的属性，如热力学稳定性和突变稳健性。RNAexinv 不仅考虑二级结构来设计序列，还考虑突变稳健性和最小自由能。生成的序列可能不完全符合给定的 RNA 二级结构，但它们将严格符合给定二级结构的 RNA 形状，并因此考虑到提供的推荐热力学稳定性和突变稳健性值。
输出结果由所提出的方法生成的设计序列组成。选择一个序列会显示目标的二级结构绘图和序列的预测折叠，包括有关所需和实现的热力学稳定性和突变稳健性的一些基本信息。RNAexinv 可以在没有先验经验的情况下成功使用，只需指定一个初始 RNA 二级结构，并用点括号表示法和所需的中性和最小自由能的数值表示。该程序在 LINUX 操作系统下运行。二级结构预测使用维也纳 RNA 包进行。
RNAexinv 是一个用户友好的工具，可用于 RNA 序列设计。在需要严格保持天然序列的功能茎环结构的情况下，它特别有用，但在其余结构中，只要保持整体形状，可以在不影响其他结构的情况下，在远处的基序中多一个或少一个核苷酸。这允许插入物理可观察值作为约束。RNAexinv 可在 http://www.cs.bgu.ac.il/~RNAexinv 获得。
