Supporting RNAstructure: Software for RNA Analysis

支持 RNAstruct：RNA 分析软件

• 批准号: 7649303
• 负责人: DAVID H. MATHEWS
• 金额: $ 21.21万
• 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 2010-09-09
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7649303
• 关键词: Accounting; Adopted; Affinity; Algorithms; Antisense Technology; Binding; Biology; Bite; Catalytic RNA; Cell physiology; Code; Communication; Communities; Computer software; Computers; DNA; Development; Drug Delivery Systems; Electronic Mail; Equilibrium; Free Energy; Gene Expression Regulation; Genetic Carriers; Grant; Health; Human; Immunity; Internet; Java; Libraries; Licensing; Linux; Maintenance; Modeling; Myotonic Dystrophy; NIH Program Announcements; Online Systems; Operating System; Output; Peptides; Pharmacologic Substance; Play; Printing; Publications; RNA; RNA Interference; RNA Sequences; RNA Splicing; RNA analysis; Reaction; Reading; Research Personnel; Role; Source Code; Structure; Technology; Temperature; Therapeutic; Thermodynamics; Update; Work; base; data exchange; design; enthalpy; file format; graphical user interface; human disease; improved; interoperability; programs; tool; user friendly software; user-friendly

DESCRIPTION (provided by applicant): RNA plays many important roles in cellular function. In the Central Dogma of Biology, RNA serves as a transient carrier of genetic information and as the adapter molecule that reads the code. RNA catalyzes reactions and serves in post-transcriptional gene regulation, development, and immunity. RNA also plays roles in human disease, including Prader-Willi and myotonic dystrophy. Understanding and harnessing the power of RNA, e.g. with RNAi, antisense technology, or with therapeutic ribozymes, requires an understanding of the structures of these RNA sequences. RNAstructure is a software package for RNA secondary structure prediction and analysis. It is available at: http://rna.urmc.rochester.edu and has been downloaded by a total of over 11,000 users. The specific aims of this proposal include both development and maintenance for the RNAstructure package: 1) Develop enthalpy nearest neighbor parameters for RNA secondary structure formation to allow structure prediction and analysis at other temperatures. 2) Construct a web server to provide RNA secondary structure nearest neighbor parameters and offer tutorials on their use. 3) Add RNAML support to the existing software to improve interoperability with other software packages. 4) Port RNAstructure to Unix, Linux, and Macintosh OS X using the Java runtime library to build a user-interface. 5) Provide high quality Adobe Acrobat File (pdf) output directly from RNAstructure, so that predicted structures can be edited for publication. 6) Update RNAstructure for 64-bit Microsoft Windows Vista. 7) Provide source code for download under an open license. 8) Construct a web server for the OligoWalk algorithm for predicting equilibrium binding affinities to an RNA target. Web servers are highly popular because of there ease of use. 9) Offer an email reflector for communication by the RNAstructure user community. This work has broad implications for human health. The computer tools contained in RNAstructure are used by others to determine RNA sequences that are good drug targets. RNAstructure is also useful for the design of RNA-based Pharmaceuticals.

描述（由申请人提供）：RNA在细胞功能中起着许多重要作用。在生物学的中心教条中，RNA充当遗传信息的瞬态载体，也是读取代码的适配器分子。 RNA催化反应并用于转录后基因调控，发育和免疫力。 RNA还在人类疾病中起作用，包括prader-Willi和Myotonic Distrophophy。理解和利用RNA的力量，例如使用RNAi，反义技术或使用治疗性核酶，需要了解这些RNA序列的结构。 RNAstructure是用于RNA二级结构预测和分析的软件包。它可在以下网址获得：http：//rna.urmc.rochester.edu，并已由总共11,000多名用户下载。该提案的具体目的包括RNAbstructure软件包的开发和维护：1）开发RNA二级结构形成的焓最接近的邻居参数，以允许在其他温度下进行结构预测和分析。 2）构建Web服务器以提供RNA二级结构最近的邻居参数，并提供有关其使用的教程。 3）在现有软件中添加RNAML支持，以改善与其他软件包的互操作性。 4）使用Java Runtime库构建用户界面的端口rnastructure到UNIX，Linux和Macintosh OS X。 5）直接从RNStructure提供高质量的Adobe Acrobat文件（PDF）输出，以便可以编辑预测的结构以进行发布。 6）更新64位Microsoft Windows Vista的RNAstructure。 7）提供源代码以在开放许可下下载。 8）构建用于寡头算法的Web服务器，以预测与RNA目标的平衡结合亲和力。由于易用性，网络服务器非常受欢迎。 9）提供电子邮件反射器，以供RNAbstructure用户社区进行通信。这项工作对人类健康具有广泛的影响。其他人使用的计算机工具被其他人用于确定是好的药物靶标的RNA序列。 RNAstructure对于基于RNA的药品的设计也很有用。