Supporting RNAstructure: Software for RNA Analysis

支持 RNAstruct：RNA 分析软件

• 批准号: 8139943
• 负责人: DAVID H. MATHEWS
• 金额: $ 27.53万
• 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 2014-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8139943
• 关键词: Affinity; Algorithms; Antisense Oligonucleotides; Area; Base Pairing; Biology; Code; Communicable Diseases; Computer software; DNA; Data; Development; Disease; Environment; Enzymes; Equation; Free Energy; Functional RNA; Gene Silencing; General Population; Grant; HIV; Influenza; Inherited; Libraries; Licensing; Linux; Maintenance; Malignant Neoplasms; Messenger RNA; Methods; Nanostructures; Oligonucleotides; Optics; Peptides; Performance; Plant Roots; Play; Probability; Program Accessibility; Publications; RNA; RNA Folding; RNA Interference; RNA Sequences; RNA Viruses; RNA analysis; RNA annealing; Reaction; Reporting; Ribosomal RNA; Role; Small Interfering RNA; Software Tools; Statistical Mechanics; Structure; Temperature; Testing; Text; Therapeutic; Thermodynamics; Time; Update; Virus; Work; design; enthalpy; graphical user interface; improved; melting; novel; novel therapeutics; programs; public health relevance; research study; response; software development; therapeutic target; user-friendly; web interface; web services; web site

DESCRIPTION (provided by applicant): RNA plays important roles in many areas of Biology. Functional RNA sequences that work at the level of RNA, i.e. not as an mRNA coding region, are called non-coding RNA (ncRNA). ncRNA sequences serve diverse roles from sequence recognition, such as hybridization in RNA interference, to catalyzing reactions, such as peptide bond formation by ribosomal RNA. To understand RNA function and to harness the power of RNA, with RNA interference, therapeutic RNA enzymes, or RNA nanostructures, an understanding of RNA structure is required. RNAstructure is a software package for RNA secondary structure prediction and analysis. It has been downloaded by over 17,000 different users and is available at the Mathews lab website http://rna.urmc.rochester.edu. It provides state-of-the-art algorithms for RNA structure prediction using the most current understanding of RNA folding thermodynamics. It also provides algorithms for finding the optimal secondary structure shared by two sequences, which is, on average, much more accurate than predicting a structure for a single sequence. Furthermore, it provides methods to predict the affinity of structured oligonucleotides (DNA or RNA) annealing to a structured RNA target. These predictions are important for the selection of effective small interfering RNA (siRNA) for gene silencing. RNAstructure is provided with user-friendly graphical user interfaces in C++ for Microsoft Windows and in JAVA for Linux or Mac OS-X. Text interfaces are provided for scripting or command line use. These can be compiled on Unix/Linux/Mac OS-X and executables are provided for Windows. Finally, a shared C++ class library is available for programmers to include algorithms in new programs. The proposal is to extend and maintain RNAstructure. Four formal aims are proposed for the next period of support. Aim 1 is to provide a new wizard mode for RNAstructure to guide users through the analysis of their sequence(s). Aim 2 is to update the nearest neighbor parameters for predicting conformational stability using the most recent experimental data. Aim 3 is to provide all the RNAstructure components via web interfaces. Aim 4 is to provide fast and accurate prediction of secondary structures that include pseudoknots, which are currently not predicted by most algorithms. PUBLIC HEALTH RELEVANCE: This proposal has direct public health relevance. We provide software tools for predicting, understanding, and targeting RNA structure. These can be applied to understanding the biology of infectious diseases because some viruses, including influenza and HIV, are RNA viruses. Furthermore, they can be used to design novel therapeutics, such as antisense oligonucleotides or small interfering RNA that both target RNA. This RNA-targeting therapeutics could be used for diseases such as cancer or inherited diseases.

描述（由申请人提供）：RNA在许多生物学领域都起着重要作用。在RNA水平（即不作为mRNA编码区域）工作的功能性RNA序列称为非编码RNA（NCRNA）。 NCRNA序列从序列识别（例如RNA干扰中的杂交）到催化反应（例如核糖体RNA形成肽键形成）发挥不同的作用。为了了解RNA功能并利用RNA的功率，需要RNA干扰，治疗性RNA酶或RNA纳米结构，需要了解RNA结构。 RNAstructure是用于RNA二级结构预测和分析的软件包。它已由17,000多种不同的用户下载，可在Mathews Lab网站http://rna.urmc.rochester.edu上找到。它为RNA折叠热力学的最新理解提供了最新的RNA结构预测算法。它还提供了用于查找由两个序列共享的最佳二级结构的算法，这比预测单个序列的结构要准确得多。此外，它提供了预测结构化寡核苷酸（DNA或RNA）对结构化RNA靶标的亲和力的方法。这些预测对于选择有效的小干扰RNA（siRNA）很重要。 RNASTRUCTURE在Microsoft Windows和Linux或Mac OS-X的C ++中提供了用户友好的图形用户界面。提供文本接口用于脚本或命令行使用。可以在UNIX/Linux/Mac OS-X上编译这些，并为Windows提供可执行文件。最后，可以让程序员使用共享的C ++类库，可以在新程序中包括算法。 该提议是扩展和维护RNAustructure。为下一个阶段的支持提出了四个正式目标。 AIM 1是为RNAstructure提供一种新的向导模式，以指导用户分析其序列。 AIM 2是使用最新的实验数据更新最近的邻居参数，以预测构象稳定性。 AIM 3是通过Web界面提供所有RNStructure组件。 AIM 4是为包括伪诺的二级结构提供快速准确的预测，这些结构目前尚未由大多数算法预测。 公共卫生相关性：该提案具有直接的公共卫生相关性。我们提供用于预测，理解和靶向RNA结构的软件工具。这些可以应用于理解传染病的生物学，因为某些病毒（包括流感和艾滋病毒）是RNA病毒。此外，它们可用于设计新型的治疗剂，例如反义寡核苷酸或均针对RNA的小干扰RNA。这种靶向RNA的治疗剂可用于癌症或遗传疾病等疾病。