Supporting RNA structure: Software for RNA Analysis

支持 RNA 结构：RNA 分析软件

• 批准号: 9762909
• 负责人: DAVID H. MATHEWS
• 金额: $ 34.65万
• 依托单位: UNIVERSITY OF ROCHESTER
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-07-01 至 2022-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9762909
• 关键词: Achievement; Address; Algorithms; Antisense Oligonucleotides; Binding; Biology; Chemical Agents; Clustered Regularly Interspaced Short Palindromic Repeats; Communicable Diseases; Communities; Computer software; DNA; DNA Sequence; Data; Databases; Disease; Enzymes; Equilibrium; Free Energy; Genetic Diseases; Genetic Transcription; Genome; Grant; Health; Human; In Vitro; Inosine; Internet; Lead; Licensing; Life; Linux; Measures; Messenger RNA; Methods; Modeling; Modification; Monte Carlo Method; Nucleotides; Oligonucleotides; Optics; Pattern; Performance; Pharmaceutical Preparations; Pharmacologic Substance; Plant Roots; Play; Process; Publications; RNA; RNA Editing; RNA Sequences; RNA analysis; RNA methylation; Reporting; Ribonucleases; Role; Sampling; Science; Secondary to; Sequence Homologs; Small Interfering RNA; Software Tools; Statistical Mechanics; Structure; Temperature; Testing; Thermodynamics; Time; Untranslated RNA; Update; Variant; Weight; base; design; enthalpy; experimental study; graphical user interface; improved; in vivo; melting; online resource; open source; predictive tools; programs; public health relevance; small molecule; software development; synthetic nucleotide; tool; user friendly software; web server

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.

项目总结： 快速测序方法确定了生命所有领域的功能RNA序列。另外， 结构图谱方法显示了RNA包括信使RNA在内的广泛的体内结构。 确定RNA结构的作用及其作用机制对生物学和人类是至关重要的 健康。RNA二级结构预测是一种常用的辅助理解工具 RNA功能，并通过开发软件解决了RNA二级结构预测的需求 包RNA结构。 RNAStructure是一个用户友好的软件包，用于RNA二级结构预测、显示和 分析。它包括用于单个序列的结构预测的方法，包括伪结点、结构 双分子相互作用的预测和多同系物的保守结构预测 序列。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，提高结构预测的准确性。它还可以预测未配对的 这些预测对于siRNA和反义寡核苷酸设计是必不可少的。 提供了RNA和DNA序列的热力学参数，这扩展了结构 对DNA的预测。这些程序具有图形用户界面(适用于Windows、Mac OS X或 Linux)、命令行界面以及Web服务器。这些算法也可用于其他 程序作为一组文档化良好的C++类。该包是完全开源的，在GNU Public下 驾照。 对于下一阶段的支持，我们提出了高影响力的目标，这些目标将使RNA结构在其 能够做出社区所需的新型结构预测。我们会更新最近的 邻居参数使用最新的实验结果，并将参数扩展到包括核苷酸 在A、C、G和U之外，这是转录后修饰的结果。我们还将扩展我们的算法以 提高伪结点预测的准确性。最后，我们将继续支持我们的用户社区 和开发商。