Supporting RNA structure: Software for RNA Analysis

项目摘要： 快速测序方法鉴定了生命所有领域的功能RNA序列。此外，本发明还 结构作图方法证明了RNA包括信使RNA的广泛的体内结构。 确定RNA结构的作用及其作用机制是生物学和人类学的核心。 健康RNA二级结构预测是一种常用的帮助理解 RNA的功能，我们解决了RNA二级结构预测的需要，通过开发软件 包装RNA结构。 RNAstructure是一个用户友好的软件包，用于RNA二级结构预测，显示， 分析.它包括用于单个序列的结构预测的方法，包括伪结、结构 双分子相互作用的预测，以及多个同源的保守结构的预测。 序列的它可以使用结构映射数据，包括与化学试剂和酶的映射， 揭示未配对的核苷酸，以提高结构预测的准确性。它也可以预测未配对的 这些预测对于siRNA和反义寡核苷酸的设计是必不可少的。 为RNA和DNA序列提供热力学参数，这扩展了结构 DNA预测这些程序提供图形用户界面（适用于Windows、Mac OS X或 Linux）、命令行界面，以及Web服务器。该算法也可用于其他应用。 程序作为一组文档齐全的C++类。该软件包是完全开源的，在GNU公共 执照 对于下一个支持期，我们提出了高影响力的目标，这将使RNAstructure在其领域保持领先地位。 能够做出社区所需的新型结构预测。我们将更新最近的 近邻参数采用最新的实验结果，并将参数扩展到包括核苷酸 除了由转录后修饰产生的A、C、G和U之外。我们还将扩展我们的算法， 提高了伪结预测的准确性。最后，我们将继续支持我们的用户社区 和开发人员。

Project Summary: Rapid sequencing methods identified functional RNA sequences across all domains of life. Additionally, structure mapping methods demonstrate extensive in vivo structure for RNA, including messenger RNAs. Determining the roles of RNA structures and their mechanisms of action is central to biology and human health. RNA secondary structure prediction is one of the tools that is commonly used to aid in understanding RNA function, and we addressed the need for RNA secondary structure prediction by developing the software package RNAstructure. RNAstructure is a user-friendly software package for RNA secondary structure prediction, display, and analysis. It includes methods for structure prediction of a single sequence, including pseudoknots, structure prediction for bimolecular interactions, and prediction of the conserved structure for multiple homologous sequences. It can use structure mapping data, including mapping with chemical agents and enzymes that reveal unpaired nucleotides, to improve the accuracy of structure prediction. It can also predict unpaired regions in RNA, and these predictions are essential for siRNA and antisense oligonucleotide design. Thermodynamic parameters are provided for both RNA and DNA sequences, which extends the structure predictions to DNA. The programs are available with a graphical user interface (for Windows, Mac OS X, or Linux), command line interfaces, and also as web servers. The algorithms are also available for use in other programs as a set of well-documented C++ classes. The package is fully open source, under the GNU Public License. For the next period of support, we propose high-impact aims that will keep RNAstructure cutting-edge in its ability to make new types of structure predictions needed by the community. We will update the nearest neighbor parameters using the latest experimental results, and expand the parameters to include nucleotides beyond A, C, G, and U that result from post-transcriptional modification. We will also expand our algorithms to improve the accuracy of pseudoknot prediction. Finally, we will continue to support our community of users and developers.