Supporting RNA structure: Software for RNA Analysis

支持 RNA 结构：RNA 分析软件

基本信息

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
项目类别：
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

项目摘要

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.

项目概要：快速测序方法鉴定了生命各个领域的功能性 RNA 序列。此外，结构作图方法展示了 RNA 的广泛体内结构，包括信使 RNA。确定 RNA 结构的作用及其作用机制对于生物学和人类至关重要健康。 RNA二级结构预测是常用来帮助理解的工具之一 RNA功能，我们通过开发软件解决了RNA二级结构预测的需求包RNA结构。 RNAstruct 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。它包括单个序列的结构预测方法，包括伪结、结构双分子相互作用的预测，以及多个同源物的保守结构的预测序列。它可以使用结构映射数据，包括使用化学试剂和酶进行映射，揭示未配对的核苷酸，以提高结构预测的准确性。它还可以预测未配对 RNA 中的区域，这些预测对于 siRNA 和反义寡核苷酸设计至关重要。为 RNA 和 DNA 序列提供热力学参数，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。该算法也可用于其他领域程序作为一组记录良好的 C++ 类。该软件包是完全开源的，在 GNU Public 下执照。对于下一个时期的支持，我们提出了高影响力的目标，使 RNAstruct 在其领域保持领先地位做出社区所需的新型结构预测的能力。我们将更新最近的使用最新的实验结果进行邻居参数，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商。